Gens KMod -> CPU -> Debug -> Layers. In most cases, layer B seems to be the "floor" (the "water" in this case). However, it replaces it with blackness (notice my tutorial video) so you need to take care to fill it back in correctly. It ought to be a minor hack to make Gens KMod fill it in with another colour, I just need to get hold of the source first.
Until then, a lot of the time, alignment with the 32x32 grid is enough to select the right black pixels most of the time, for the rest you need to look carefully at screenshots without those layers disabled. The tile slicer/splicer might help there, but I don't use it myself.
For these beach ones, I magic-wand the water areas, then expand the selection by 5 pixels (in Paint Shop Pro), then do a colour-keyed replacement with a pattern brush based on the 32x32 water pattern.
I rarely complete a whole map in one shot, as shown in the tutorial. Instead, I merge multiple passes into each other, moreso in cases where autostitching fails a lot.
