Can you please explain what you mean by one midi controller/keyboard 'overriding' the other?
Also, if you are trying to play more than one controller at the same time and trigger sounds from different synths, then you DO need to assign which input midi controller each midi track should use. So, if I have 2 controllers and two midi tracks, and controller 1 is supposed to control piano, and the other is supposed to control strings, then change the Input assignment for each midi track to point to the corresponding controller you want to have triggering notes for each of the two synths. In this example, assign the Input device for the piano midi track to be controller 1, and assign the Input midi device for the strings track to be controller 2.
If you make assignments the above way, AND these are not 2 instruments loaded into a single instance of a multi-timbral soft synth, then it should work fine.
When I DO have multiple instruments loaded into a single instance of a multi-timbral synth, such as Kontakt 5, I then will assign particular midi output channels (just under F/X bin in a midi track), to keep the responding instruments in Kontakt triggering only notes for the intended instrument.
Hope any of the above helps,
Bob Bone