One of the biggest advantages is that if you have a tile, you can assign it a number and use it as something like a stamp but the kicker is that if you edit that tile, any other tiles assigned to the same number will change with it.
What I did in the case of Metal Man and Clash Man was right clicked the pic in vgmaps and copied it into PyxelEdit. I would turn on the tile grid to differenciate the tiles then any time I saw a different tile, I would hold Ctrl then click on it to assign it to a number. It will show the tile as a stamp on the right hand side for later use. Since I got a pasted, I placed the numbered tile in place of the matching tile. When it is all said and done, all I got to do is color in that specific tile and the rest is history. I can also see which tiles I missed easier. I coulda used this program when I was doing Woodman's stage.