There are many professional booksellers that maintain an active presence on ebay both for the selling and the buying of inventory. If you believe ebay's hype theirs is the only marketplace that matters on the internet.
Although I do occasionally sell, and even more rarely buy on ebay, and I've also experimented with there very pricey ebay stores option, for the most part I've, (forgive the pun) opted out of ebay. The reason is not so much based on their fee structure or even the fact that I seriously resent the zeal in which they try to shove the use of Paypal down dealer's throats; it is due to the fact that I'm a compulsive auction watcher, if I have an item listed or I'm planning on bidding on an item, I'm constantly checking the listing and sulking if I feel the treasure I'm selling is not being appreciated. Believe me sulking in a woman my age is not an attractive thing.
More succinctly, even without compulsive auction watching or any other form of procrastination, no small book selling operation will be able to do equal justice to all online markets, the decision of where the majority of effort should be focused is a personal choice and a bit of a moving target.
Promoting your own website, Amazon, Alibris, Abebooks or other database sites, ebay or some of the smaller auction sites, offline catalogs, presence in a brick and mortar location, blog promotion, acquiring inventory, there are myriad areas demanding attention and the amount of attention needed will not only vary with the type of operation but also with the time of year. At its best being an independent book seller is as much of a balancing act as a high wire artist performing without benefit of a net; awesome when everything is going smoothly but always one small miscalculation away from disaster.