> The raw files assign the tile to be used for an object in game, and certain objects have hard-coded colors while others also have colors assigned in the raw files.
Yup.
> For what I'm concerned with (stairs, walls, rocks) gray scale tiles will take on the color of the material used to build the object (example; stairs dug out of bauxite will be red) and the gray scale will be used to hue the pixels to darker or lighter shades of red.
Yeah but there are various exceptions and ways of overriding color.
http://df.magmawiki.com/index.php/DF2010:Color> Anything drawn in the full tile-set file in color will remain that color in game no matter what.
Only if the game draws that tile with white as the foreground colour. See below.
> Tile-magic summed up; There are two colors available to be assigned to a tile, foreground and background. Black used as background frees up the settable background color to be used basically as foreground color 2.
Not quite. The foreground tints everything, which you can play with (see
this post) while alpha transparency allows the background colour to show through - doesnt matter what the colour is, which again you can play with.
> So, what I need cleared up is how to make the transparencies, and also how to determine what will be assigned foreground and background colors. And how to make the black so that it won't accidentally get colored...
Cant help with the how-to of working with alpha channels in gimp, but they are the key.