First just fills in flat colors on a level under the lineart. I used a really large brush set at the softest level and shaded over what I wanted to be shaded. Erased anything the dark color went over it wasn't suppose to and then used a soft eraser to blend the dark shade with the color I went over. Used a lot of layers so if I made a mistake would be real easy to fix.
Micron pens hardly bleed and especially on the smooth paper I use. That's also the main reason I use such small pens. I very carefully go over the edges of the lines to smooth out any little bumps or distortions that could have occurred. Which is also why my lines are so thick...they don't always start out that way but grow because I made a mistake. Use photoshop to make the lines darker and look more flat. Also erase any stray lines or dots that might have happening during inking.