You can use SH3Cmdr at any point in your career without any problems.
The Rollback Function in SH3Cmdr is there to make sure that you "clean" your installation from all the files SH3Cmdr has put into your SH3/GWX directory. Use the Rollback function before you Enable/Disable mods (you have to be at Port to alter the mods) and your installation will work fine.
Foe more information I do suggest you read the brilliant SH3Cmdr Help file and the FAQ Jaesen put with the program. It does answer all your questions.
If you still have problems or you're not sure about something give us a shout
