I've replied to this here, since it seems more appropriate than the 'Secret Project' thread where it first appeared:
Mardroid. For future ref, you can choose two colours per layer in Manga studio (I'm using debut 4..). The layers need to be colour layers, though.
This isn't right. You're creating grayscale layers, then changing the
display properties to colour, then choosing the "Alternative Color for Black" option to tint the grayscale layer.
You need to create a colour layer in the options when you first select "New Layer":

Once you've done that, you can work on the colour layer in as many colours as you like, although I should note again that MS lacks a CMYK mode. You get a very limited colour picker in Debut (it's more useful, and includes swatches and the ability to save your own colours in EX), which you access from Window -> Color

Cheers!
Jim