I have been using Sprite to restore everything after I flash a new rom, I have been using Merge Level 1 with no issues.
If you have some things you dont want to restore to your new rom just uncheck them in the tree.
The only issue I have had is restoring did not work 100% when I went from WM6.1 to WM6.5.
If you restore and it screws things up just clear storage and try a lower merge level.