I don't even do that, the M&LSSS+BM sprites have conveniently sized spaces around them that are the same size (across frames of that particular animation) so I just delete the color around the sprites and create actions that move the image so far left > duplicate animation frame > move image left again, eventually moving it to the beginning of the next row, etc
I'm not sure if you can do that in GIMP (i use Photoshop) but if you can, that eliminates the risk of having some frames a pixel or two off position. Making multiple layers works better when there isn't an equal distance between each sprite though.