directory location of sync files?
For the first question, I think its actually stored under C:\Users\username\My Music\iTunes\iTunes Media\, if everything is standard. If anything, it will be wherever your music is also stored (just in another directory). 

As for your second question, I don't think you can tell it not to sync the apps. The only ways to not keep them would be to delete off your iPad before sync, or delete from the file system after sync.