Just so you know, what shortcuts i'm using:
Ctrl+o, open a file. (batchrename a set of BMPs to same name with small addition to it, so you can put the edit in the same directory as the to-be edited files. This way you save the switching between directories.)
Ctrl+o: open second file.
Ctrl+a,c,w,v,zero: select all, copy it, close file, paste, make image fullscreen in one action.
Erase everything you dont want on the upper layer.
Index the image with image/mode/index colours. (make a shortcut with edit/edit shortcuts (very down in menu)).
Tap Enter twice.
Ctrl+s, ctrl+w: save picture, close file.
Rinse and repeat.