You can see some of the mistakes I made in the inking. Here’s a scan of some line art before it was touched up. If you are printing the seps out on an inkjet printer like we do, it doesn't matter much. I do the separations in either RGB or CMYK mode. Keeping the edge non-anti aliased makes selecting the lines easy and doing the separations easy and accurate. Once the art is totally black and white with no grays I touch up the art with the pencil tool to keep the hard edge on the art. If the line art is too light I will use the Brightness/Contrast adjustment to darken the lines before I use the Threshold adjustment. I scan it in Grayscale, import it into Photoshop and use Image > Adjustments > Threshold to change the image to a bitmap and eliminate the anti-aliasing that makes the lines fuzzy, playing with the setting to get the line weight I want. If the art is closer to the final size I might use 400 pixels/inch. I have a pretty tight drawing style so I sometimes draw the art smaller than the finished print size and scan it at 600 pixels/inch. The resolution depends on what size I drew the art.
Once the art is finished and the pencil lines erased, I scan it at a pretty high resolution in Black & White Grayscale mode. I'm not trying to produce an original masterpiece, just a good final product and fast is better. If I make a mistake, I usually draw the correction right through the mistake and fix the line art in Photoshop.
Both the regular markers and the brush markers. In case you are wondering, I sketch the drawing and transfer my sketch to Graphics 360 Marker paper with a mechanical pencil, tightening the sketch as I transfer it, and then ink it with markers, mostly Pigma Micron. Still have a bunch of Rubylith in a box somewhere. I’ll give up my Adobe Photoshop when they pry it from my cold, dead fingers. Of course, you can do color separations by hand and cut the film, but I did that for way too many years before we had computers. Here are a few examples of how I do color separations for silk screened posters in Photoshop. Note: The information here is for people with some familiarity with screen printing and computer graphics, specifically Adobe Photoshop.