I say to calibrate each of them individually because, especially when they are located in different locations in the room, there is no way of knowing how much each will contribute to the total SPL without first calibrating them individually to "get a feel" for each one's contribution that total.
You also need to set the phase of each sub to the mains individually too. And then just to make sure, with each other. Otherwise, you could have a situation where you're getting cancelling, and that is worse than no sub at all.