Well, you could try using the FX system. I had been experimenting with it for the past few weeks and it's really cool! Basically in the FX file, you could use the easier multitexturing method, or you could also choose the low level shader programming to create some nifty effects. I had managed to use the FX system to create a per pixel bump + specular mapping for my game, I will post it here soon.
I can post the FX file code snippet to do what you want here if you wish to. Generally, alpha maps can be coded easily using multitexturing.
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