Once you have your files converted to a BMP heightmap, you can tweak it by changing single pixels. The format for the pixel values is simple:

Height = R (0 to 255) + G (0 to 255) + B (0)

It's not trivial to assign a particular height to single pixels! If you imagine that two pixels with RGB(0-2-0) and RGB(1-2-0) are displayed as almost similar shades of black, but represent a height difference of 256 meters, you know what I mean...

BTW: In case you have a 32bit BMP file, the fourth Byte of each pixel will always be 255.