Hi Neil,
The "Use Auctiva Store Window" seeting only need be enabled if you would like the store window to be automatically added to your listings.
It is definitely okay to leave the store window setting disabled in your account if you are manually adding the store window to your listings. This will have no adverse effects on the functionaltiy of the store window.
Perhaps the "Use Auctiva Store Window" setting should be renamed "Auctimatically Add Store Window".
-Mike