Suprisingly, compared with Amazon and Barnes & Noble, Apple's publishing system is by a wide margin the most confusing, slow, and difficult process you'll encounter, even if you already have a Mac. Admittedly, the iTunes Connect Mobile app (which lets you check on your book sales via your iPhone) is a nifty addition to the package. On the whole, however, if you're considering using an aggregator at all, the complexity of Apple's process is the best reason to pay for that kind of help.
One option with ebook selling is to let someone else do some of the work. You still have to write and format your book properly, but after that's done, the aggregator works with the reseller on your behalf, freeing you from dealing with accounting, ISBNs, and signing up multiple times on each service. In fact, Apple openly encourages the use of an "approved" aggregator in its service FAQ, likely due to the headaches outlined above.
You can find many aggregator services. I checked out two for this piece, Smashwords and Lulu. In general, the process is about the same as working with retailers: You upload your manuscript, a cover, descriptive terms, and payment information, and then the aggregator takes over. Aggregators coordinate with the retail sites, and they sell the books directly themselves, as well.
Smashwords is a somewhat scrappy startup, and next to the polish of Amazon and Apple, it looks a little quaint (the site is a bit buggy too). Smashwords will prepare your ebook for just about every platform known to mankind, including Kindle, Nook, and iOS, plus Kobo, Sony Reader, Stanza, Borders, and more. Commissions range from 80% for books sold directly through Smashwords to 60% or less for books sold via other merchants, as Smashwords takes a cut of each sale alongside Amazon or Apple's cut. After all is said and done, you could be earning about 50% commissions in the worst possible scenario.
To sell with additional merchants, your book must meet Smashwords' rather strict guidelines for "Premium Catalog" inclusion. Unfortunately, two weeks after I submitted my book, I was still waiting for the approval process to complete, with no ETA received. That is vastly longer than working with the merchants themselves, but given the likelihood of someone actually buying a book directly from Smashwords and manually syncing it to their ereader device (instead of having it automatically downloaded for them from a retail ebookstore), it's certainly worth the hassle if you're planning to go this route instead of selling to a retailer directly.