I wrote up a fairly comprehensive article about my colouring process since lots of people were asking about it, which you can check out here!
(I would be great if you did, I spent FOREVER writing it!)
A quick summary, however, is that after doing flats and adding in little details I visit my big library of watercolour textures and find appropriate ones, and mess around with them on a multiply, overlay or screen layer
Then I add in shadows with a multiply layer, and a luminosity layer if there is a really obvious light source (my comic has a fair number of candlesand mysteriously magical glowing things!) I also use the clipping group function on SAI to colour bits of my lineart, especially things that are distant in the background: