Do just one at a time, less chance of mistakes that way. Make a line on the hull that is accurate for each shaft to follow, then offer up a shaft and tube, making sure you have room for the motor after the tube has been fixed in and that the prop will be the correct distance from the stern. When you are satisfied everything is accurate, put a LITTLE superglue on the join, just to hold it for a while. now is the time to double check all is well. When that has set you can finnish the joint with p40. Take your time to get a smooth strong bond. I put a little sellotape on the outside first and work filler through from the inside, this saves sanding off too much filler later. When that has set build up a neat strong fittet on the inside.
When both tubes are in you can make your motor mounts and align the motors. If that presents difficulties get back to us, it’s one of those jobs that’s easy when you have done it but seems tricky when you do it for the first time