I started to respond to this yesterday when I found this thread, but I realized I didn't have anything coherent to say. I haven't tried to approach the stores like Fictionwise, so i don't know their policy regarding accepting work directly from writers, but I understand some of the smaller companies do accept writers' work directly.
The biggest issue an independent writer has with the bigger sellers is promotion. This especially includes Amazon, and it's something I found during the year I had my books in the Kindle store: If you don't have a lot of money for advertisement, or if you are not a major publisher with written contracts with Amazon, you are unlikely to be noticed among all the bestsellers and big name books out there. Amazon's tags and recommendation engines can help, but even they are skewed towards the big money players. That's why indie publications in the Kindle store (or any big e-book store) can be all but invisible to casual visitors, or anyone who isn't specifically looking for you or your work.
You'll likely get more e-book exposure at smaller bookstores, but they get fewer customers... that's why they're small. (It's one of those "vicious circle" things I've heard about.)
But Beth already has a publisher (which is more than I can say). The biggest value publishers provide today is exposure. Without them, you're much less likely to rise above the crowd and be noticed. Print, e-book, it really doesn't matter if no one ever sees them. If you already have a publisher, e-books probably won't make that much more of a splash for you... you might as well go with your publisher's plans (or no plans) for e-books, or feel free to suggest things (like free giveaway e-books), but accept the publisher's decision on them.
If you are brave enough to stand up to the publisher (and risk getting dropped), be aware that you'll end up doing a lot more legwork, and in the long run, the publisher probably would have done better for you. But if it means having more control over your product, it might be worth it to you to go that way.