Erm, I saw that Dan Magaha is telling that 800x600 wouldn't run with Civ 3, and if it did, it would only be visible screen part, blah blah. Well I think the issue is old, however, here's a link to the solution for it I posted at Apolyton in December... if you need it, enjoy.
http://apolyton.net/forums/showthread.php?s=&threadid=38888
http://apolyton.net/forums/showthread.php?s=&threadid=38888