If you do it properly iso - with a consistent 30 degree line grid, then you can make that line up with a hex grid. Now that won't get your measurements quite right when moving, but it will snap to grid properly. With some careful token construction it can look very very cool in maptool.

Looking great so far. The iso map was fun to do - but I'd recommend putting in the horizontal level markers to keep the viewer informed about the different levels.