Hi Taulukos,
Welcome to Auctiva! Auctiva Checkout can only be applied to listings that are posted through your Auctiva account while Auctiva Checkout is enabled, so the listings you had posted prior to joining Auctiva will continue to use eBay Checkout. The only settings you have to configure in your eBay selling preferences to ensure Auctiva Checkout works properly are your "Combined Shipping" and "Combined Insurance" rules.
It is not currently possible to send invoices directly through Auctiva, so you will want to continue doing so through your "My eBay" page. When sending an invoice, you should choose the insurance specification that is appropriate for the transaction. For example, if you want insurance to be "Optional", select "Optional" when sending your invoice, because the invoice data will override what was initially specified when the listing was created.
While we do not offer any inventory management tools yet, we do currently offer support for eBay stores. In order to create an eBay store listing through your Auctiva account, you just need to check the radio button next to "store item" at the upper-left of the Auctiva lister page. You will then be able to choose the expanded durations and other details associated specifically with eBay store listings, and will be charged for those listings according to the eBay stores fee structure.
Any additional questions or concerns? Please file a support request using the approrpiate link on our help page: http://www.auctiva.com/free-auction-software-help/help.aspx
-Mike