Yeah, Smashwords is frustrating that way :\ I had uploaded two books, IIRC, before I realized that they had my name in as "Clare Miller" instead of "Clare K. R. Miller." I changed it on my account, since that was the only way, but then the books had to be resubmitted to the premium catalog and one of them never made it to Apple again as far as I can tell. I've since started distributing to Apple through Draft2Digital, which is much less frustrating. I recommend D2D for iBooks and B&N (since you obviously go direct to Kobo and Amazon). The only downside is that only via Smashwords can one make a book free on B&N.

I know it is possible to make your account on SW into a publisher account that can publish multiple pen names, though it's not clear how one does that from what I read.