you should be able to project a premultiplied rgba image if that's what you mean. If you want to mask out the result then one of your options would be using a Merge node attached to the output of the Render node to multiply it with your matte (or using "in" or "mask" mode depending on which channel the matte is in and which pipe is connected to it).
As for quick layering: if you're on 4.7 there is a Keymix node that just takes A, B and and alpha, otherwise you can always copy your matte into one of the images and use a Megre node set to "matte" to put it on top of the other image (or premult it manually and use "over"). There are lots of other ways of achieving the same thing though.