I'm currently working on a comic with a friend, and my plan is to color it in photoshop. I hand draw it and scan it, but when it comes to putting the lines on a new layer, I'm stumped. I'm too used to drawing the lines on the computer, not scanning and coloring. I also just opened up the image in photoshop and it wouldn't let me use the layers... don't know what happened there.
First you need to make sure that your image is in RGB or CMYK mode. If it's limited palette it won't let you do layers.
Image -> Mode -> RGB or CMYK
As for moving lines to a new layer,
1. Scan/cleanup (it's important here to make sure your blacks are fairly good and solid)
2. Select all, Copy.
3. New channel (channel, NOT layer), paste, invert (ctrl-I), load channel as selection (the small dotted circle in the lower portion of the channels window).
4. New layer, fill with black. Turn on transparency lock. Deselect.
5. Delete original lineart layer or just fill it with white.