I'm in a similar situation myself. Am upgrading my receiver, and going from a 5.1 setup to a 5.2.4 setup. I'm keen to have Atmos, and also the benefits of 2 subs.
I currently have a 10 month old Polk Audio HTS12 sub-woofer. Have been quite happy with it.
Initially I was interested in trying out a different brand, but my reading all points towards matched subs, and avoiding subs with different characteristics.
So I'm assuming I am restricted to adding another HTS12. Correct me if I am wrong please?
If you're wondering what receiver I intend to use, its likely between the Denon AVR-X3600H and the Marantz SR6013. Both have individual configuration for the subs.