I have 2 subwoofers but under different brand, although my Yamaha amp got 2 subs out but to avoid different phase and bass cancellation, I connected one SVS PB2000 to sub out and Polk Audio sub to the center speaker. The sub just located next to the front speaker and the bass is Omni directional, so the placement is not so important. I adjust the frequency to max on the sub and carefully adjust the subwoofer volume to get the most natural effect(not over bass) that I want. When you watching movies, the voices are thick and with action movies the effect is superb like the bass punchy directly on to your face.
I learned this from my friend who is the technician get involve in setup many commercial cinemas in my country. According to him, for commercial cinema, each of the speakers is attached with individual subwoofer to get the best cinematic experience. In our home, if we have the extra subwoofer we can do the same. Usually start with center speaker and next is surround speaker. Center speaker attached with individual subwoofer will create the feel of thick speaking voices and action movies with more punchy bass and if attached with surround speaker, this will help to enlarge your soundstage.
You try it sure you will love it!