Scott,
Assuming you belong to both, once you certify L1, L2, or L3 in either organization you can send a copy of the signed certification form to the other organization’s HQ and you will receive the same certification level. You don’t have to fly two different certification flights. You should still fly as many flights as you can, but this way you don’t have to worry about failing the second flight.
I do belong to both but certifying for both gives me more excuses to fly with different groups, even if I fail one or two.