"Can I use two different subs in my system?" This is a question that always seems to come up in classes... and for good reason.  Its much easier to buy an additional sub than to buy two new subs.  The answer is not always easy.  For example it depends on just how different the subs are.
For obvious sub differences like power and driver size the big problem is that the sub layouts used by the HAA depend on a true balancing of capability.  Subs need to be sound balanced for the best results.  A sub that is louder than another will defeat the desired push-pull nature of the sub interaction.  Its also very difficult to match the sound level of two disparate subwoofers.  Bottom line is that you are making your calibration much more difficult.  Difficulty in calibration often means no true calibration is completed. 
In the case of subwoofer mismatch the great results that the theory predicts may actually not occur.  My advice is to use the same identical subs in sets of two or four.  You'll end up with a great sonic result and be able to do it in a reasonable amount of time.