For the colour I'd suggest one of two ways forward. One is to get yourself a nice textured background - like a parchment and use that to get rid of the white. Then set a layer to overlay (again, under the lines) and use a very light yellow to lay in the highlights and a very dark blue to lay in the shadows. Then use a low opacity brush on a colour layer to set the colours over the top.
The second approach would be to find a nice grungy brush, turn on wet edges and set it to low opacity (around 10-20%). Then start laying in the colour. Start with light shades, and then move on to darker shades. That should give you a nice watercolour look. The grungy brush will stop you being too precious about edges and will lend a texturing to the piece which will avoid it looking too photoshopped.
Experiment, and see what you like. Post what you've got here and I'm sure people will chip in with ideas of what they feel works and what doesn't.