Now back in photoshop, it's time to set up your basic layers. First, double click on your background layer. Name it linework.

Next, create two more layers. Name one Base Colors. Now select your unnamed layer. In the upper left corner of Photoshop (not your layer palette), find your Layer dropdown menu and select Layer/New/Background from layer. This will turn your unnamed layer into your background layer.

Now select your linework layer. in the upper left of your layer palette, it will say normal. Click on the drop down menu and select multiply. This will allow color to be seen through your white areas while keeping your black lines intact.