Does the key stay in the start position or does it automatically go back to run when you released the key, momentary switch? If it stays in start I would wire it so you turn it all the way to start to run on battery then turn back to run for magneto. As long a battery voltage is isolated from the run post you should be ok. Check your your meter. In any case you do not what a long pause between switching between the two, boom goes your muffler if not fast.