Well, I only know one way of coloring so far. What I always do is make the sketch and start erasing and shaping up the lines. Or some other times I just remake the lines again completely over the sketch in a separate layers.
After I´m pretty much happy with the lineart, I set the layer style to multiply and if I want the lineart to have a darker tone of the base color, I go to Image>Adjudgement>Levels (I use Photoshop). And at the output level bar I move the left pointer to the right, this removes the pure blacks.
And for coloring, I just set a base color on a layer below the lineart, and with a hard edged brush I start setting up the shading. After that, with the eyedropper I choose the color inbetween both, chance it to a slightly saturated color to give it some life and the then blend the colors with a slightly softer brush.
If you use a mouse, the best method to blend colors would be to set the opacity of the brush to around 20-30 and then pick the inbetween color and click like crazy.
Kinda long and unorganized post, if there´s anything specific you (or anyone) wants to ask, just ask away. I´ll try to be as helpful as I can.
Also, here´re some tutorials I always found REALLY helpful:
http://www.itchstudios.com/psg/art_tut.htm (and since we are at it, here there is a link with some megaman fanart by the same guy
http://www.itchstudios.com/psg/main.php?id=megaman)
And this one, which explains a lo better the lineart part:
http://conceptart.org/forums/showthread.php?t=109491