I'll try to forward the question to the mailinglist as I'm not very authorative with such configurations.
I think there are several ways to solve this. Setting up different midi send channels for your keyboards is necessary if they are connected on the same midi device.
On the midi track you are recording to you can setup which channels they are listening to. Check the [input routing] button in the TrackInfo for the midi tracks. Tip: hold [Ctrl] to keep the input routing menu open while making changes.
Do let us know if you have further questions as this was probably unclear.