Scan in a grayscale drawing and adjust levels as desired. Select All and Copy the image.
Create a new file. File New. The size of the image will be the size of the image you copied.
Open the Channels pallette. Create a new channel. The default name will be Alpha 1. Select the Alpha 1 channel and Paste.
Return to the Layers pallette and make a new layer. Title the layer "line."
From the menu bar go to Select > Load Selection. Choose Alpha 1 and click the invert box.
Choose a color other than black. Option + delete (on a Mac) will fill the selection with the foreground color.
Hide the Background layer and you will see that the elements that were white in your scan will be transparent.
At this point I lock the transparency on the line layer. This allows me to paint the line any color I would like with a basic paint brush (the red in the above image is an example of painting with a basic brush with the transparency locked).
Painting on the background layer will look like this.