1. I work on 9”x12” smooth Bristol
2. We have a large Epson perfection flatbed scanner that can scan the whole page (and more)— however all pages before 82 were scanned in 2 parts on a tiny cheap HP all-in-one printer/copier/scanner that was a hand-me-down.
3. Depending on the details on the page, the first thing I do to the art is adjust Levels and/or Brightness and Contrast until the lines are as dark, crisp and detailed as I want against the white. The blue will be there still, though it’ll be a lot more saturated and sharp. Then I’ll open up Hue/Saturation and edit Cyan and Blue and turn lightness all the way up and saturation all the way down. Then I desaturate the lineart or convert it to grayscale.

Oh my goodness!

Well, personally I stick with the blue lines because they’re kind to my eyes, but the way the pencils are removed from the finished page is done in a way that you can use any color that isn’t black or gray. I tried green and purple before, and while they still produced clean line work, they hurt my eyes too much.

This is the make of lead I use: http://www.jetpens.com/0.5-mm-Color-Pencil-Leads/ct/368

I use a Platinum OLEeNU mechanical pencil because colored lead tends to break easily, and these pencils are designed to prevent breakage. It isn’t a perfect fix, but it saves me some heartache.

I’m not sure what you meant by hiding a line. Or a “line I didn’t want to ink.” These lines are very light, I darkened them in that picture for visibility, so they are very easy to draw over. And, like I said, I stick with a light blue because it’s easy on the eyes.

I assume maybe by “hiding” you meant making it disapear when scanned. What you’d do is knock the brightness and contrast up a bit to make the blue a little more pure, but not enough to distort the black lines. Open Hue/Saturation,  drop down Cyan (or whichever colors you’re trying to remove) and raise Lightness all the way up, Saturation all the way down. Sometimes you have to do the same with the Blue, if there are still remnants where the pencils were particularly dark. Then, if you aren’t going to reduce the image to Grayscale, Desaturate the line art instead to remove any other hints of color.

I hope that was helpful!

EDIT: I should also note that the guidelines for the layout, bleed and panels is done with Copic markers in a similar color to my pencil.