If you are looking to purchase a custom domain for your Auctiva store or your eBay store (if you get one), you can definitely do that through Auctiva. If you purchase a domain through Auctiva, you could actually have it point to your Auctiva store initially and then adjust it to point to your eBay store if you end up getting an eBay store and decide you would like to do so.
If you think you might want to use your domain for a purpose other than your Auctiva store or your eBay store, it would be best to purchase the domain through a registrar like GoDaddy or eNom and point the domain to the site of your choice because there would be a fee to use your Auctiva purchased domain to use it for a separate purpose.
Also, the main benefit that getting an eBay store would provide is that it would allow you to post "store item" listings which are charged according to the eBay stores fee structure outlined on the following page of eBay's help index: http://pages.ebay.com/help/sell/storefees.html. "Store item" listings are fixed price only, have longer durations like 30 days and "Good til Canceled", and are charged lower insertion fees and higher final value fees than regular fixed price and auction format listings.
