some cydia tweaks arent compatible with ios6. I ran into more than a few issues with tweaks I use on my ipod. Math alarm, weather icon, gridlock, etc dont work on ios6 yet. Torch worked at first for me, but then the update made my phone boot in safe mode. If your installing tweaks one at a time, it makes it easier to find what is incompatible. In the description of your installed packages, it should show what its compatible for, and you may also check the changelog. If its from 2009, it may not be compatible
As for backup and restore, if you do it through icloud it will not backup cydia stuff. So by doing that, it will backup your official items and when you restore it should just go back to a stock iphone. I had to do that with my ipod touch when updating the firmware from os 4 jailbreakme.com to a os5 redsnow one. After my phone was restored, all my official apps and settings were still on there. What I lost was all my cydia stuff. You can just take screenshots of all your cydia tweaks-- remember to install and then try one at a time so you can locate ones with issues. I believe you can also log into cydia and have it save your downloaded items for exactly what your trying to do.