I create my terrain in paint.net as a multi layered bmp file so I have elevations. I do it first in colors to keep track of the elevations while mapping everything to 8pixel=1mile. Then I bring those layers into Krita as 16bit grayscale png where sea level is 1000 grayscale and max elevation 33000 grayscale. When I have converted my color layers into grayscale by copying from paint.net and pasting into Krita, I flatten the image and export as a krita 16r. I rename the extension to RAW and import into ImageJ where I export it as an unsigned RAW. The terrain editor recognizes that format and pops me up a terrain.
After that I make the map file and if needed add a layer from the original png or bmp blueprint to keep my terrain features on track like river valleys and canyons as I work the elevations. Cranked out fjordma in 4 months because of that.