I am in the process of building a 4 engine CL profile scale project with electric power, so I have double trouble compared to a twin.
I have been running the motors on the test bench and basically I have a separate speed control, battery for each location. I am using electronic controls for throttle so I have one reciever that feeds the same signal to the all four speed controls. The 4 way harness splits off the reciever signal to all four speed controls. Each motor is a stand alone unit each having a motor, battery and speed control.
You might be able to get by with one timer with a 2 way Y-harness, just make sure both speed controls are programmed to respond to the timer the same way. I am using e-RC speed controls from Hobby Lobby and I have to program them so that they all are matched and respond the same to the electronic control system I am using. When I move the throttle stick from motor off to idle all four motors start up and idle the same, I then can bring up the throttle on all four electric motors.
It might be worth a try to hook up two stand alone motor, speed control and battery combinations being controlled by one timer. That way it will be the same timer and RPM setting for both motors.
Good luck,
Fred Cronenwett