Whenever I use Civ3Edit, overlays such as cities and goody huts don't appear, but right clicking on the square says that the overlay is there. In the game, they appear right where I put them but they dont show up in the Editor. Does anyone know why and how I can fix this?

Try pressing Control+Shift+M (just like clear map in the game). It'll show those overlays. You can also get to it from the "Map" menu in the editor.