To know which color index goes with which terain/altitude, open maptrans.txt in your /dragon/script directory. You'll see stuff like this:
Code:
// ****************************
// 00 = Grass
// ****************************
00 00 000 0003 0004 0005 0006
01 00 005 0003 0004 0005 0006
02 00 010 0003 0004 0005 0006
03 00 015 0003 0004 0005 0006
04 00 020 0003 0004 0005 0006
05 00 025 0003 0004 0005 0006
06 00 030 0003 0004 0005 0006
07 00 035 0003 0004 0005 0006
etc...
Each line tells you about one index from the palette file. The first number is the position in the palette. The first digit is the row, the second is the column (from 0-f, in hexadecimal). The next number is the group, in this example, '00' is grass. Next comes the altitude. I tend to stick with multiples of 5, but that's all personal preference. Then you have the landscape tiles, which are selected rendomly from the list.
So, to place grass at an elevation of 0, use the color in position '00' of the palette. This is row 0, column 0, or the top left color. As another example, the index '4a' would be the color from row 4 (remember, we're numbering from 0, not 1) and column a (or 10, in decimal).
You can change what's in the maptrans.txt quite easily, just make sure you keep track of your changes in the palette file as well.
As for indexing, create a new image, 6144x4096. Then go to Image->Mode->Indexed, select custom palette, choose the palette you pulled from the osiconversion image, **uncheck "Remove unsed colors from final palette"**, and click okay.
Open the palettes dialog and double-click the osiconversion palette and you're off and running.