Hi Mcfalgan,
To do this, you need to calibrate each sub individually. Once you have calibrated one, make a note of what level the amp has it at, preferably as close to 0db as you can.
Then un-plug it and calibrate the second sub on it's own, making sure that you end up with the amp level being the same as the previous sub.
You can do this by adjusting the gain on each sub. Then when the two are both connected they will be at the same level.
Hope this helps.