Using Categories and syncing

Hello all, First time jailbreaker and so far I do enjoy it. I have used Categories to help clean things up. Put about 35 games in one folder and all my jailbreak apps in another. I used purplera1n on my 3G S 32GB with 3.0 and everything works wonderfully. My question is when I go to sync my phone or back it up do I need to remove all those apps from the Categories folder or can I just sync like normal. I know with purplera1n i can do that, but wasnt sure how Categories might come into play.

Thanks