For submission purposes, it doesn't matter. No multipliers (countries and zones) are called out in the Cabrillo log. The contest sponsors determine those from the callsign.
As far as getting SD to score it right...I'd check with the SD mail list/reflector. Click "Contesting" in the left menu area of this page (takes you to www.contesting.com
), then go down to near the bottom of the next left menu you get and you'll find a link to the SD mail list.