You could also make a new brush that makes 1 white pixel with 4 pixels of another color (I think dark would work better than light). This would make the capital pixels more visible even without extra layers, and while playing. The Faerun maps' capitals are done this way, IIRC.
The Faerun map's capitals are done by painting a star around the white spot (a solid ring of full 0, 0, 0 black and then adding single pixels at the cardinal compass points). Did those by hand and then copy-pasted an entire 5x5 block into the palces where I wanted them.