when you are making your listing on auctiva, there is a check-box near the 'template' section... you click it IF you want your store window to match your template. if you have customized your store window, and don't want it to match the template, UNCHECK that box. then you can have the template you want AND the cust. window you want. hope that helps!!
let me know if you need something else! edit//// as for your store front matching your window.. that's a lil harder. there are many store templates and a few have different color choices. they are not as customizable as the window. if you REALLY want them to match, i think your best bet is to come up with a storefront you like, then build your window colors around that. however, your window and store never appear together, so i personally think it's not really necessary. like in a real store, i think it's nice if your 'window' is more like a sample of what's in the store, rather than a miniature duplicate of the store. the store window IS seen with your auction, so i personally think it's more important for THOSE to match. just my opinion!
ps.. if your auction is already active, i don't think 'just' changing your saved listing will change the live auction. i have changed my window, but it has never shown up if my auction is already active. you'll either have to get the html to change the listing, or worry about it for the next one.