my process is, uh, A LITTLE COMPLICATED. xD I go back and forth a lot since I use blue lines pretty heavily. This is from my cover banner, but it's the same process I use on my comic!
I'll usually do a very rough sketch on computer to get the composition the way I want it in a form that's easy to alter. Then I edit the whole picture to be cyan blue and print it out, and draw the pencils on top of it! I use basic cardstock for everything, since I gotta be able to run it through my printer (Bristol board is a little too bulky for the printer I have).
But then I scan those pencils in, remove all the cyan from the image, so that I just have the pencil lines, turn THOSE lines blue and print it out again:
(in case you're wondering: a lot of times if there's extra room on the page, I'll just print out a doubled version of the blue lines, in case I mess up and need to start over)I really love inking. Inking with ballpoint pen is absolutely not the most efficient method, but I just enjoy it so much, and I like the results I get from it, so I do it anyway. xD
Once I've scanned in my inks I'm done with the traditional part of my usual process!
I prefer not to mess with the settings when I scan, since I'd rather do any edits in photoshop, so I just scan the image in full-colour, as--is. Then I fiddle with colour channels to remove the cyan from the picture so that just the inks remain, clean up the inks a little and touch up any mistakes I made digitally, and then do all my colouring in Photoshop!
When I'm doing comic pages a lot of times there's also an extra round of refining the pencil lines, where I scan in rough pencils, add perspective lines in Photoshop, and then print it out blue again and pencil over it again -- but FOR THE MOST PART this is my very back-and-forth process as it stands now! xD