You can still sync with iTunes, you just have to be VERY careful when the iTunes updates are going down. The best way to handle the updates is to undo the JB and accept the update when you are ready. Many wait until the update already has a new JB version in place. Accepting the update while still JB can cause some pretty annoying issues with the phone and should be avoided pretty much at all costs. Sometimes it will just install and knock out the JB, other times it can lock out the phone and you've got to get some heavier time invested into getting it back up and running again.
So in short, yes, still sync, but must watch for iTunes updates.