Hi,
I agree it is probably best to have each running off each motor. The problem is you go to the fuel dock twice as much which can be a PIA if there is high traffic. The other is you actually double the opportunity to get bad gas as you go to the dock twice as much. If there is a 3% risk, it is now 6% but the impact is 50%. The impact is probably the same - boat needs to be pumped and checked out.
So in my opinion it is a coin flip. The more you use the boat, the more the fuel dock trips if you are filling one at a time.