Kinda depends on what, exactly, you’re trying to do with the program. Since you’re asking me I’m going to venture a guess you’re a comics person too? If you want to know my basic process, I start on paper. 11 x 17 comic paper. If you hate erasing you can use blue pencil lead. I kinda rotate. Draw up your page. I ink with a pentel brush pen. Panels are usually done with sharpie since I want the lines to be solid and straight. I have a large format scanner (it was about 200 bucks). It saves me from having to either a) scan my pages in pieces or b) draw on under-sized comic paper. 

Once you get your scan, I suggest you clean it up a bit in Photoshop. I play around with the brightness and contrast so my dark lines are darker. Save it and pop into Illustrator. All my ink lines are vector traced. Open a canvas and do file—>place. From there it’s literally just the image–>trace option with ‘ignore white’ selected. This gives you just the black lines. If they look good to you you can just select them all and then drop them back into a canvas in Photoshop. My stuff is 350 DPI. It will import it as a vector which you can’t edit unless you decide to rasterize. Then it’s just building up layers behind your drawing for the colours. I generally do just the flats on one layer. Darks on another. Lights on another. If there’s weird effects (like when I draw Chamber’s glowing veins) they get their own layer too. Word balloons are the top layer. I shove all text in a folder because it can absolutely get out of hand if you don’t. 

That’s the bare bones process for me.