When drawing with pen and coloring with watercolor it is important to use a waterproof, bleed-proof, india ink pen. I like to use Faber Castell's Artist Pitt Pen. I draw the image first, wait a few minutes for the ink to completely dry and then paint in the colors. Another key is to use transparent watercolors. If you use opaque colors chances are you will cover up the ink lines.
1. Draw first with india ink.
2. Paint with transparent watercolors.
Simple as that and makes a cute little painting. Don't worry about filling in every inch of paper with the paint because that adds to the character of watercolor and ink.