By default, DundJinni works at 1 inch = 5 ft at 200 DPi.

To make maps that work well with Maptool, I export my map as a 100 DPI Bitmap. I then open it in Photoshop, click on "Image Size", make sure the map is the right size at 100 DPI and save it. When I import it to MAptool, the system grid and the map grid usually line up.