I found this colouring tute for PhotoShop that uses transparency masks and fill-layers to colour lineart.

Here's the PS Tutorial - www.melissaevans.com/tutorials/colouring-line-art/3

It can be duplicated in GIMP, which I'm trying at the moment on one of my own linearts.

For moi it makes colouring easier and allows you to keep track of each colour in each part of the image. And makes it easier to change out a colour simply by doing an overall bucket-fill, once the layers are set-up.

Shading should be a breeze too.

I like it.

~ Pyre

Another link for a great digital painting crash course by artist TsaoShin.

Painting in PS, but can be applied to other digital drawing programs too.