Moving applications and OS to SSD

Honestly, I think you are making it way more difficult than it needs to be. While you can manually manage the location of files (OS and Apps on the SSD and everything else on the HDD) and there are certainly some people that do, I don't think its worth the hassle. Create a fusion drive and let the OS manage everything. I doubt you personally are going to be more efficient at manually managing the file system than a modern OS.

 

Creating a fusion drive isn't difficult. Tons of tutorials around the web. It may be intimidating but its not difficult. In fact, I would say what you are proposing to do is much more difficult that creating a fusion drive. However, I will say that I thought you were putting both the SSD and the HDD in the mac mini. It sounds like you are not reinstalling the HDD in the Mac but instead intend to use it externally. I don't know if that will work for a fusion drive. It would probably work but if the external drive gets disconnected, the whole thing will stop working.
I'll try and answer your questions specifically.
1. No, I don't think so. You can't just drag your system folders to new locations. I would think that you would need to clone your HDD to the SSD with CCC.
2. Yes, you can move your libraries for the apps (Photos, iTunes, etc) to different locations like the HDD. On my MBA, my iTunes library lives on an SD card.
3. I don't know why you'd need/want to partition your SSD. Whats the advantage?
4. Why do you want to have 3 different versions of Mac OS? If you're concerned with space, that is going to take up a huge amount of space on your SSD. And if you really did want/need to be able to run different versions of the OS, virtualization may be a better way to go.
5. Yes, Disk Utility will let you make a new partition on the fly. Always make sure yo have a full system backup before you start partitioning your drives.
6. Yes. Point and click.

 

Whether you want a fusion drive is up to you.

Do you mind "managing" more than one drive icon on your desktop?
Or in the case of a partitioned HDD, perhaps three, four icons, each representing a different volume?

Or do you want it "all in one" (volume)?

Some folks seem to have trouble with multiple volumes.
Others have no trouble at all.
This is a decision ONLY YOU can make.
(I prefer multiple volumes, each with its own purpose.)

Having said that...

If all you want to do is to move everything from the HDD to the SSD, use a disk cloning app.
Either CarbonCopyCloner or SuperDuper will do this job quickly and easily.
Don't "overthink" this.
Cloning an entire volume is as easy as copying a file or folder, IF you use the right tool for the job. Just takes a little more time.

I like CCC because it will also create a clone of the recovery partition onto the SSD, as well.

I would recommend that you keep the OS, apps, and user accounts on ONE partition. This is fine for the SSD.

IF you have LARGE libraries of music, movies, or photos, you might want to consider keeping these on the HDD.
These are the kinds of files that are usually not accessed that often. Storing them on a platter-based HDD makes little difference, because great "speed" isn't necessary to access them.

I keep my Mini's internal HDD set up like this, with no less than FIVE partitions:
1. Boot (backup of SSD)
2. Main (main files, banking, frequently-accessed files, etc.)
3. Music (mp3's, etc.)
4. Media (books, a few mp4's)
5. General (copies of OS's, copies of apps, other stuff that isn't really "important", but of which I'd like a copy)

This works for me, even though it might confuse others...

 

I just tried to use CCC with my daughter's MBP, but apparently it doesn't transfer over the boot loader, so when the SSD is installed internally, powering up displays a flashing folder icon with "?", meaning it's not bootable.

What's the point of having CCC then?

 

Every clone I've made with CCC has been bootable. Mine included the recovery partition also. Are you sure you had the options set correctly?