I'd have both subs on, since both will be in use at the same time.

If you want to get a bit picky, you may turn the test tone on and run each sub alone. Adjust each sub using the sub amp's gain control until the two give the same level at your listening position. Then you could turn both subs on and adjust the trim at the 990. Some of the dual sub users may have some first-hand feedback on whether that extra step is beneficial.