Hopefully you've already figured out that option B (AVR sub out 1 ----> MiniDSP Input 1--->Route all subs to input 1).
It took me some time to understand the goal of multiple subwoofers. At first I thought more subwoofers equal more bass. And I also did not understand that no matter how many subwoofers you have, the goal is also to set them up in a way that the AVR "sees" them as ONE BIG SUB. As I've learned more and dove deeper into this hobby, I've come to learn that the true benefit of multiple subwoofers is to even out the frequency range of the bass and also increase the headroom. This means that if you have only 1 sub, then based on its placement and the location of the listening position, unless you are extremely lucky, there is a good chance that there will be nulls in your frequency response as well as some peaks. These issues aren't always detectible with just the ear (listening), but they can be easily detected via measurement equipment such as a MiniDSP Umik-1 microphone and REW. This measurement process has a learning curve, but if you are willing to learn, it can be very rewarding as you learn what is going on in your room and where the problem areas are. Once you know where the issues are, you can move the sub around and or adjust the listening position until you find best spot for both. IF there is still an issue, you can either live with it, or look to add subs in order to fill in the gaps. Again, this will introduce another learning curve worth exploring, because there are programs such as MSO (multi Subwoofer Optimizer) for which there is a beginner thread here at Audioholics, which can really help fill in those gaps via software and your MiniDSP 2x4HD. If you have more than one listening position, the need for multiple subs is increased. The more subs you have to fill in the gaps, the more seat to seat consistency you will have. This of-course requires that you learn how to combine all of the subs so they end up sounding like ONE BIG SUB that happily fills the room evenly in the listening areas. If you want to learn more about how to do this via MSO, here is a link to the thread.
MSO for Beginners Thread on Audioholics
Good luck and happy listening.
Wellz