Hi, It's been a little over a year since I took on this project and I finally have mapped all the areas in the game. I do plan on putting them all together into one big map shortly.
I cheated in the Maridia area, because I could not find a Photoshop filter that would work with the water layer. For all the other areas Photoshop had the perfect filter for water and lava that looks almost identical to the game. However nothing was even close for the way they did the Maridia area. So I just left the water out... to make the map more clear and legible
Some point I would like to get the water in there, but at this time I don't see how to do it. At least not without spending another year just on that part
As an added note, I did use SMILES export to bitmap function. However I needed to recapture most of it using vSNES to get the transparent areas to insert the backgrounds. However SMILE did help give me a template to work with.