If the starting battery gets low, can you install a jumper from the posts on the starting battery to the positive and negative posts of one trolling motor battery in a 36 volt system, and leave it there until you get home and get it on the charger?

What kind of motor do you have? I've used jumper cables and jumped my starting battery off one of the trolling motor batteries. Once started, the alternator charges the cranking battery back up.

+1

250 SHO - I can jump it off as well, but if you are in a tournament and don't have much running to do, why not leave the jumper in place, so that the aerators are pulling off the trolling motor battery as well as the starting battery. I know it will work, but I don't know if it will damage anything on the motor, such as alternator, voltage regulator, etc. Can anyone tell me?

won't hurt a thing but you will run the trolling battery down, if it gets too low you will cause the trolling motor to heat up due to low voltage.
just jump it when you have to or get a backup battery for the acc.

There is one issue jumping the cranking battery off of a trolling motor battery. DO NOT JUMP IT IF:

Sonar electronics is using the internal transducer (Universal Sonar) within the trolling motor.

Grounding the cranking battery ground (which is the sonar unit ground)to a trolling motor battery ground can damage the TM's internal transducer circuit.

In an emergency, be sure to disconnect the transducer cable from the sonar unit before jumping the batteries.

I just pull a troll battery and switch with my starting. The deep cycles have plenty of cranking amps once the motors already warmed up

Thanks for the replies guys. How about some of the boat mechanics on here. What will it hurt to run jumpers from the starting battery to a trolling motor battery and leave it in place all day while you fish, run the boat and use trolling motor?

You can use a perko switch to do this.