I always work with grayscale maps, as I find it easier to work with just one color than to remember what reds, greens, blues, etc. will do in RGB maps. Sometimes old school is the best way. To begin a region, If I'm creating a fictional region, I determine what dimensions will facilitate my overall vision, and multiply 64p, 128p or 256p +1 to achieve the ideal size. I'll be using a single 256p tile for this demo. The base color has been adjusted from the games default base, so as to minimize the "denting" of the terrain by ports and other lots.
1. Load your map into photoshop. You can copy this map to your pc. This is a completely level tile. I usually use no more than this, but for the sake of the tutorial, I have broken this down to individual steps.
2. Just add water. Darken your map by adjusting mid-tones. .02% up or down = about .15m in game. Black, obviously, is as deep as you can go. This is set at about -1.5%. Semi-shallow.
3. Shallows. You can make these any way or where you want, and as many as you have the patience for. For simplicity's sake, this will be a 2 depth transition. On a separate base map, cut out a shape you want, adjust the mid-tones to preferred depth, copy and paste to the master map.
4. At this point, you have 2 options. Blur the 2 waters now, for a crisp, accurate coastline, or add in the land mass and blur all together for beaches and such. Add your land now.
5. Click on each individual layer with ctrl key, and use your blur to meld them together. Less blur will give you a more choppy look, more will give you smoother transitions.
The end results-