First, DO set up all profiles within Auctiva (i.e. your Paypal email addy for one) This will save you MUCH time when you create new listings, you won't have to type in the info each time.
The Auctiva store is just one of the freebies you get with an Auctiva account...however if someone comes across your store and clicks on an item they will be directed to the ebay listing. I never pay attention to the Activa store, it has nothing to do with your Ebay store.
(Auctiva ECommerce Stores are a whole different thing, totally 'stand alone' and seperate from Ebay) You can see a whole Community section here devoted to this topic.
You can use ebay checkout (I always have, just find it easier) but still be sure to have your profiles filled out on Auctiva. Check your account preferences here and be sure to DISable anything you don't want or understand because it all comes ENabled.
It does take a little while to get the hang of things here but when you do it's totally worth it. You'll be breezing through listings in no time
Good Luck!