Making a TwbT tileset's actually a bit more work, since you need to make more tiles...
Honestly, I always found it easier to just hand-draw tiles than to try repurposing old ones.
But anyway, the short of it is that color filters what is on your tile. This is why tiles are generally white with some gray shading - a blue color will turn off all red and green, leaving only the blue aspects of the color, so if you have a patch of the tile that is red or green, that patch of the tile will appear black, instead.
You also want transparency, because many tiles, when printed in the game, use the transparency layer as a second color. For example, in the basic Curses tileset, a standard dog is a brown "d" on a black (transparent) background, a war dog is a gray "d" on a black background, and a dead dog is a brown or gray "d" on a dark red background. The transparent section turns dark red upon death.
Many more recent tilesets take full advantage of this - for example, Phoebus recolors the bushes in the raws so that a harvestable shrub uses a "bush" tile with (opaque) black on the edges, and transparent "berry" sections. Then, most forageables have a color of green for the primary color (that the actual tile gets colored) and purple or whatever the berry's color is for the secondary color (which is where the transparency goes).
Download Phoebus's tileset, or others, and put the "art" file in GIMP or Photoshop where you can see the layers, and test it out in action. Just create a new layer under the main layer, and set that to whatever your "secondary" color will be, then alter the "main" layer to be whatever colors the actual material will be.
Again, keep in mind that material tends to determine the color of tiles. Some stone is white, some is brown, most is light or dark gray, and you occasionally have large swaths of cyan microcline in your dining hall.
Finally, graphics for creatures is totally separate, and does not have any of the filter rules apply, so you can have full-color images for dwarves or dogs or keas or whatever.