Together as one or individually
These words might not sound very important but will make a huge difference in how your receiver treats and calibrates your subwoofers.
Parallel
If you have a receiver that has two subwoofer outputs that are in parallel, your receiver essentially treats both outputs as one: They both receive the same signal. That will be limiting, as the room correction software won’t be able to optimize the subs to their full potential if they’re placed at different positions.
Individual
If your receiver has 2 or even 4 individual outputs, you’ll be able to calibrate them independently from each other, meaning each sub can get the appropriate distance (delay), level, and EQ depending on where it’s positioned. This will make all your subwoofers – not only perform better on their own – but also integrate better with the rest of your system.
Which is better?
If you only have 1 subwoofer, a parallel output is perfectly fine. If you have two subwoofers but stack them on top of each other, having parallel outputs will also be perfectly fine. It’s only when you have multiple subs placed at different locations throughout your room you will benefit from having individual subwoofer outputs.