Step 1:
First I start out with a rough sketch, usually just armatures or some vague features so I can get an idea of the figures and composition.
Step 2:
Now I go through and fully draw the outlines, erasing guide lines and sketching in the backgrounds. I trace the outlines again, making them as dark as possible in lieu of actual inking.
Step 3:
Once everything has been drawn, I shade the characters. You want to be very clean and bold when drawing a digital comic in traditional media. I like mechanical pencil and either bristol or pen-sketching paper as they allow for cleanliness and small details. These are drawn on 8.5x11 paper. That's pretty small, so I need to be able to get those details in.
Step 4:
Now I scan the page and set it into my frame template. I set the 'frame' layer to 'multiply' so that the black shows up and the white disappears. The frame isn't the same shape as the page, so the top and bottom get clipped a bit.
Step 5:
Since my scanner's pretty crappy, it scans too lightly. I go to Image > Adjustments > Levels at the top menu to fix this. Twiddling the arrows below the graph will make the darks darker or the lights lighter, relatively. I darken it up so those blacks stand out.