MOST airplanes need a little right rudder just after liftoff, to compensate for engine torque, P-factor/gyroscopic precession of the rotating powerplant masses/ and-or onboard evil spirits.

If the water rudder is in the left float, it will cause a drag toward the left, so you will already have some right-rudder dialed in assuming you were able to hold the plane straight on the takeoff run.

If the water rudder is in the right-side float, you may lift off with some left rudder, causing the airplane to be in a cross-controlled configuration, low, and slow all at the same time. Things can get real bad, real quick when that happens, and you might have to go for a boat ride.

However, it's not all bad. The water rudder SHOULD NOT be in the water except when you are taxiing slowly. Once you are up on-step, it should be high and dry, and it shouldn't matter which float it's on. Check your WR, and see if it sticks down more than the height of the step (1/2-3/4") below the transom of the float. If it does, you can trim it or adjust its position, or at least install a kickup rudder that will ride out of the water at high speed.