If you wanted to run dual subs, I would split the signal out of the subwoofer jack on your receiver to both subs, set all speakers to "small" in your receiver, adjust the crossover on each sub to its max setting (or disable it if you can). Match the sub's level's as much as you can (if you have an SPL meter, this is really easy to do), and balance it with the rest of your system.
Your Pioneer's default internal crossover setting is 100Hz, and doesn't appear to be able to be adjusted lower than that. It has 150Hz, and 200Hz setting beyond that. If you're using small satellite or bookshelf speakers, this setting will need to be adjusted according to their low frequency response (higher than the lowest speaker frequency, if you will). Make sure all speakers (regardless of size) are set to small, and your receiver's crossover will be directing the proper low frequency signal to both subs at the same time. This avoids "cascading filters", which could introduce phasing issues, and simplifies having to adjust each sub independently.
Try it out and see if it works for you.