I'd not be inclined to used 2 different subs - basically the sound mismatch. As for the onkyo, you could use the sub out for one, and a pre-out for the other. Of course it would make setting up a mess.
I'm surprised Onkyo had an issue, you are just outputting a raw signal. Lots of people use 2 subs. But, heh, it's their product, they should know best.