Unfortunately I don't think you can do this. If you look at a brush, you can see it's just a grayscale image. Where it is black, the brush will lay down the current foreground colour; where white, it is transparent. Shades of grey give the foreground colour at less than 100% opacity.

So AFAIK there is no way to have the brush lay down one colour in some areas and another in different areas (I'd love to be proved wrong though!) What you can do is to paint your stiches on a new layer using the colour you want for the stitch itself. Then you could lock transparency on that layer and with a small round brush paint over the parts you wanted to be another colour (e.g. red). You can do this as much as you like with different colours- locking the transparency will ensure you never paint outside the pixels laid down by the original brush. It's very easy with a tablet.

Steve