Balancing monsters against other monsters?

I'm a DM that will be building several encounters for my players, but there is a catch. They will have assistance from some allies out of the Monster Manual, but those allies will be various CR's, as will the enemies.

Has anyone found a way to match CR's against each other?

EDIT: These methods you all have suggested sound easy enough to apply. I think I'll try it out in a dummy setup and see how they play out.