We have two cobranet networks on site, and only one nControl.
My question is: Should either of these networks be connected to the nControl? (if so, which one?)
Both networks have CABs and NIONs on them. I know CABs should be assigned to the nControl, but what is the suggested practice with two cobranet networks? Should any CABs be assigned to the nControl, or should they stay assigned to their respective nions?

There is no requirement that the CABs be assigned to the nControl.
Since I like to stay consistent in my design, I would leave the control of the CABs to the NIONs (instead of one VLAN the NIONs and the other VLAN the nControl).  Being consistent is always a suggested practice!
Hope this helps,
Fergy