Noob question about backups and restoring JBen settings

Some of you may have read my other thread about foolishly deleting the stock YouTube app from my phone, and then struggling to get it put back. At this point, it looks like my only option is to do a full restore, let Apple install it back on fresh, and then re-JB and work back to where I am now. However, I question how easy/possible this is.

The main problem is I don't know how exactly iPhone backups done through iTunes work. If I do a backup of my phone right now, JBen and everything, does it preserve all my apps/settings/modified files/etc? That is, does an iTunes backup make an identical file backup of the entire phone OS, regardless of what's on there? Is it the equivalent of using Carbon Copy Cloner on my MBP?

I assume that it doesn't, otherwise things like pkgbackup wouldn't exist. I bought pkgbackup and gave it a quick lookover, and it seems like it only backs up certain packages and sources, but not much else. How does pkgbackup handle specific app settings, such as SBSettings Toggles, position of apps in Iconoclast, or themes that I manually SSH'd into Winterboard? For instance, in the list of packages that it backs up, it doesn't show my current theme (which I spent hours perfecting), Suave HD.

Rambling aside, my basic inquiry is this: Is it possible for someone to restore their phone to factory settings and then easily use a backup method to get back all their JBen settings/themes/apps/sources/etc back EXACTLY how they were before? Like the title states, it's a noob question, so bear with me

Thanks guys.

 

Do you think my best bet would be to just copy my entire phone file system to my computer, and then manually SSH files that don't get backed up automatically?

I think I may just scrap YouTube. I barely ever use it anyway.

 

Yeah, I definitely learned this the hard way.