The colouring-in was done with Derwent watercolour pencils, an alternative to normal watercolour. The subtle colours seemed right for this usage, which I'd originally thought about doing in black and white and felt didn't need shockingly bright hues. For a stronger colour another time, I might try experimenting with the Inktense pencils in the same range.
There are a few more pictures from this article on my portfolio page here, but to see them all you'll have to buy Pretty Nostalgic #10, Nov/Dec 2013, available in WHSmith and many other shops.