No, there should not be much of a wait when you do a deletion. That should go very fast.

What version of the software are you using? There's a known bug where it won't reboot during a synch if you're using beta 11.

And you SHOULD be able to copy things around willy-nilly as long as you're doing it totally inside of EMPLODE. If you drag songs from the Explorer onto emplode willy-nilly, then you're going to get duplicates.