More info is needed: Do you have the LCD digital gauges? When you mention clearing the line, do you mean a small diameter hose that runs from the motor to the helm? To answer your question, the motor that sends the speed data is the one that has the signal connected. That really doesn't help. If the rigging uses a small tube that runs from the engine to the helm, on one motor there will be a small hose coming into the powerhead area, That hose will connect to another hose that runs into the rigging tube if the signal is being used. If the speed data ( water pressure) on a motor is not being used, the tube from the lower unit will have a plug in it to prevent sea water from spraying onto the powerhead.
The 'input' signal for the speed is the pitot tube, a very small hole on the leading edge of the lower unit below the anti- ventilation plate. There is a hose inside the mid section that connects either to a hose to the helm or connects to a pressure sensor that send data to the gauges.
In either case, if the pitot hole or tubing are clogged you will not get speed data.
That said, you shouldn't rely on the motor's speed data. You are much better off getting speed data off of a GPS multifunction display
