Right now, you can just drag and drop the parent directories into Emplode and it'll upload the whole thing for you, in one huge operation.
If you drag the whole thing a second time, then the problem is that it'll make a second copy of everything, which is what you don't want.
But the good news is that version 1.1, due out soon, will do dupe-checking on uploads, so that when you add new albums it'll allow you to drag the whole thing and it'll upload just the new albums, skipping the duped ones. At least, I think it'll do that, that was the plan as I recall.
In the meantime, you can simply drag the individual new albums onto emplode every time you buy a new CD. That's what I do. In practice, this isn't really that hard, it takes only a few minutes to locate my new albums, drop them onto emplode, and do a synch.
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Tony Fabris