I *think* I understand what you're asking. Unfortunately, there's only so much help anyone can give you. To be able to blend colors well, you have to develop an eye for what colors go well together, and for light/shadow.
The only tips I can give you on that is that 1) It takes more than 2 colors to blend well. 2) Colors should be very close to each other, but not necessarily so close that you can't see the difference. and 3) Colors should get lighter closer to a source of light. With a top-down view, this light would (presumably) be the sun, so colors would be *darker* for low ground, and *lighter* for high ground.
What you also want is for someone to say "Fill the red spaces with THIS color, and the white spaces with THAT color," and so on, and hope that it will blend perfectly. No matter what colors you choose, that won't work. Your lines are too rigid, and it would take many irregular layers to blend properly.
I'll show you a mock up (Using part of your image). It won't look great, but it's the *basic* process.
I pretty much just scribbled everywhere, but it's still a pretty pink mountain
If you just want a place to *start* looking for your colors, a fairly natural green that I start with, and usually change, is #2d5f2d. Remember... keep the colors in the same range... the crosshairs on the color selector in GIMP are a good guide if you're new at this. You can just click along the line to find your next shade
As for your map... All I can make out here, really, is your land vs water areas. What I see is a very interesting shape, but the edges look... i don't know.. too rounded?
I like the islands (the ones you colored) ... not sure what the white circles are around them but it's a little distracting.
I think you're off to a good start, but I'd focus on developing your map before you work on the coloring