in photoshop, paste the grid and put it to about 10% opacity, it should be barely visible. then, in another layer, use a fill can set to "use all layers, contiguous" and click click click. it's a drop at a time but it's a non-destructive way to preserve the working grid. (edit - as opposed to all of those other destructive ways of preserving )
pure hixels - my grid (the difference of hues makes it easier for me i think, gray they run together sometimes)
grid overlay with working doodle beneath.
this, i think, is the best method. tried it and i liked the fact that i could recolor one hixel in a group of same-color hixels. its hard to dither (hither) with these. :/
im working on Captain Falcon, heres my ref:
im working with this under my hixels. would that be considered illegal?