Sorry for the dumb question but this is kinda new to me:...Thanks for any answers and for not making me feel stupid.
Lets start here. There is a huge difference between being dumb or stupid, and being uninformed. There is no shame in either, but the smartest thing you can do is to ask questions (and one of the dumbest things is to not ask), so that in my book defines you as definitely not dumb or stupid. Uninformed I can help you with. I get paid (not nearly enough) to handle these issues on a professional basis regularly, so I feel that I can give you an informed opinion that is based more in fact than opinion.
1) Is remuxing just putting the MKV in an MP4 container without any compression?...
Probably; but...not...quite; and it depends. "Remuxing" is short for "remultiplexing". Compressed digital transport streams, for instance, can contain multiple programs in the same stream, and although all of the bits interleave into a big pot, the metadata that is in the packet headers keeps them organized rather than all jumbled up.
If you receive a 6.1 channel and a 6.2 subchannel from WXYZ-TV, they have
multiplexed two programs [a "program" refers to all of the separate elemental streams of audio, video, and metadata associated with a particular media element] into the same stream, or
combined two programs into the same stream. Your HDTV receiver contains the ability to
demultiplex, or
separate out 6.1 or 6.2. So remultiplexing, which is actually very uncommon both professionally and in the consumer world, is just recombining two programs or two elementary streams into the same MPTS (multiple program transport stream), at least in the MPEG transport stream world. And strictly speaking, that is not in itself, a process that requires encoding/decoding/transcoding or compressing, although any of those things may happen in a particular workflow along with remuxing.
If you do a Handbrake rip of a consumer DVD, you are probably doing a lot of demuxing. IOW, you are keeping the main video, english audio track, etc. and separating out and discarding all of the other associated streams such as second audio, descriptive audio voiceovers, added features, etc. That is one way of getting a smaller file size without compromising quality. Handbrake may not refer to it as demuxing
per se, but under the hood that is exactly what is happening.
Mp4 and MKV are both containers, or ways of encapsulating encoded media, normally to achieve compatibility. They are protocols for wrapping media, so in reality the differences between them are slight. Its confusing because both codecs such as MPEG-4 and MPEG-2 and Cinepak are usually designated by file suffixes, and wrapper or container formats are also. But a wrapper is really just the protocol for how the metadata in the packet headers is described, while the codec defines how the payload, the media, is actually constructed.
If I can take a stab at an analogy, think of a
wrapper format as just the
package your iPad came in (if you change the package it doesn't affect the iPad), but think of the
codec as
the iPad itself, and the
apps and files on your iPad as the
encoded media. What is important about that is that if you change the wrapper from one to another, it is usually easy to do and non-destructive to the payload (because you are only changing the protocol for how the payload is described). On the other hand, if you change the codec, if you chain the source and target codecs together, there is a generational loss in quality, possibly minor, possibly severe (because you are fundamentally changing how the media is constructed).
So it is important to know just what you are doing when repackaging digital files. Are you transcoding? Just rewrapping? Are you deinterlacing? Everything you do will have certain levels of consequences, from severe to invisible, depending on lots of variables including what the process itself actually is doing, the original quality level, and the target quality level, at a bare minimum. This is not a simple environment to understand and work within.
2) Grainyness has nothing to do with 1080p vs 720p right? I purchased Mission Impossible 3 1080 on iTunes and it looked fantastic but it has a "grainy" look. Is that because its filmed on film rather than digital?
1080p vs 720p will typically not have anything to do with graininess, assuming the encoding is done with a similar level of care within a similar bit budget. But if the original was a "grainy" print, 720p, by virtue of its lower resolution, will mask that particular artifact better than will 1080p or 1080i.
Film vs digital is difficult to compare because they are different processes, but there is really no shortcoming of either that makes one better than the other. Film can be done in a way that creates excellent masters, and so can digital.
If everything else is held equal (and I can't stress the importance of that statement enough) 1080i and 1080p and 720p are perceptually very nearly equivalent. No one in a double-blind test has ever been able to say "Oh, that video is 1080i and that other one is 720p and that third one is 1080p" just from watching the video play back; the differences are very subtle and even trained eyes can't approach doing that.
Generally speaking, 720p has fewer motion artifacts due to its higher frame rate and no interlace error, and 1080i has fewer static artifacts due to its higher resolution. 1080p24 has the advantage of 1080i resolution but no interlace error. That would seem to make it better than 1080i, especially if there is pulldown involved, but the slower frame rate of 1080p24 is far inferior to 720p60, so it has a lot more motion artifacting than that, and more than 1080i. You need 1080p60 (which is really only available to consumers in gaming at the present) to reap all of the separate, slightly different benefits of 720p60, 1080i30, or 1080p24. "1080p" has sadly become more marketing hype than anything else, and all of that is confused by the fact that we buy "1080p" TVs, which is completely unrelated to the display format 1080p.
3) Does something filmed digitally like Avatar have more benefits to doing 1080p or even a huge MKV rather than an older film like Back to the Future where the source is grainy and already looks just fine on 720p?
While the sheer number of variables means there is no true empirically-correct answer to that exact question, this hits on one of the basic rules of encoding/trancoding/compressing, which is the better the original is the more you can compress it to get a similar end result than if it were a bad original in the first place. So the answer is a very-qualified yes.
Another basic rule is to not use more algorithm than is needed. If a movie telecine transfer is not all that sharp, it really does not make sense to use a higher-resolution target format (1080), because the lower-rez format (720) will give the same result or even a better result in a smaller file size, and with the other benefits that 720 has over 1080 such as no interlace error, no judder/pulldown issues, etc.
As a professional compressionist, I have to understand very keenly all of the particular benefits of all of the different tools at my disposal, and know how to choose the proper set of those tools that fits both the condition of the original and the constraints of the target format, for each instance. Consumers dipping their toes into these sorts of things need to have the same level of understanding to achieve pro results.
...my Beauty and the Beast MKV was 20GB so subler would just make a 20GB M4V? Why would I want a size that big rather than a handbrake 1080p thats 3.6GB?
File sizes are only indicative of quality levels when comparing similar codecs; for instance, the quality of a MPEG-2 file may be the same as an MPEG-4 file while the file size of the MPEG-4 file may be 30-50% smaller for that same quality level. But strictly speaking, changing the file wrapper (MKV to M4V) without changing the compression level or codec would preserve the quality. The only reason to do that might be because of an incompatibility of the target player with the original wrapper format.
You may want a 20 GB file just because you want better quality, but that may not apply if the original is not that good in the first place, or if the differences between that particular source codec and the destination codec chosen make a particular level of quality impractical for a particular target file size. The situation always dictates the parameters, and knowledge of the tools is necessary to achieve the best results with the least compromise. For instance you may want to instead go for a Handbrake rip at 3.6 just because of the portability factor; you can get more movies on your iPad for that trip to NYC if the file size is smaller. Each case is unique. And if you know what you are doing, you will not have to compromise much quality to do this.
Experiment. Find what works for your job parameters by trying different things, which can leapfrog a steep learning curve if you are really only interested in a particular sort of task, such as rips for an iPad, or whatever. Of course the more you understand the more targeted the experimentation can be, but you are only limited by time and motivation.