Ok, here is a quick run down of what I do to prepare my work for photoshop, starting from the idea of the composition.

1. I lightly draw the rough outline of the comic onto paper.

2. I go over it with detail, creating the finished look of the characters.

~NOW HERE IS WHERE YOU CAN CHOOSE WHAT TO DO!~
3. A. I scan it, load it into photoshop, adjust the brightness/contrast settings to make the lines darker and I print it out. I then retrace it onto a blank paper with a blue colored pencil. Once it is done being traced, I go over it with a black ink pen. I rescan my work, and set the scanner to save it as a gray scale piece. The blue lines shouldn't show up now. Now load it into photoshop, turn the mode to RGB and your ready to go. If the lines are still rough, you can play around with the levels to make them smoother.

B. I ink the drawing if it is smooth enough, and erase the pencil afterwards. I scan it as a gray scale image, adjust the levels to make the lines smoother and get rid of any left behind pencil marks. If need be, clean it up by hand.