My problem is that if laurels8.mp contains a full set of contours, hydrography and land cover my 6324000.img file shows a corresponding 07250732 quadrangle, but if laurels8.mp consists only of ways, there is no quadrangle for 07250732. Therefore, while I can see the ways in MapSource, I can’t use MapSource to select the ways only maps to combine with my other maps.

I think that this is expected for transparent maps. As far as I understand it you cannot select anything that does not have a polygon behind it so your land use polygons, so I'm guessing your land use polygons are allowing you to select the ways in the first example. Transparent maps don't have a background polygon so you can't select anything from them normally. So I think that is just how it works and there is nothing we can do about that. If anyone knows any different though, please shout up! ..Steve