My hypothetical question - if I were to upgrade from jailbroken iOS 6.1 to 6.1.2, do I need to restore/upgrade, jailbreak again and then download/apply all the tweaks individually one by one?? Or is there any way to backup all my tweaks, restore-upgrade-jailbreak, restore all the tweaks?
You are correct. You do a restore/upgrade, then restore backup, re jailbreak and then install all your tweaks again. I only do this if there is a major upgrade or if there is a small upgrade leading to something I want. For example in IOS 5.0.1, you could not delete photos out of photo stream and that really bugged me. In 5.1.1, you could delete from photo stream. So I updated. The main part of the update was to cover 3G problems on certain mobile devices and an exchange bug.
You can read more here about it:
http://www.gottabemobile.com/2013/03/08/ios-6-1-2-bugs/
If you do want to update then there are backup apps out there for all your Cydia tweakes, apps and themes. I always used to go through my Cydia packages in Cydia and take screen shots of each page just to be safe. Here is a list of the Cydia back ups, which is the last thing you do once you have restored, re jailbroken your iDevice and then installing the backup app you used:
http://www.inspiredgeek.com/2011/09...plications-games-settings-jailbreak-required/
I have always used xBackup because you just press one button to back everything up, plus it backs up your springboard layout. Then you just press one button to restore everything. It's doesn't look like much, plus it's quite cheap. But it's very capable and reliable! Oh, and always do a full reboot once its finished even if it all looks good.
There is also a new one called openbackup which is free however I have never restored from it, so I can't honestly say its worked for me. I've seen other members here that have it installed.
Hope this helps!