I have three lifepo batteries hooked in series to run a 36 volt trolling motor. Do I hook up anywhere on the series or at the third one
The negative and positive points that are farthest away. You want to treat it as if its just one battery. All of your series connection are irrelevant. All that matters are the negative and positive terminals furthest away from each other in the bank. Another way to look at it is you want any charge or load to feed or draw from the bank as equally as possible. For more info check out Victron Wiring Unlimited. Its a must read for anyone messing around with this stuff. Theres a section specifically on what you are asking.
If you take a digital meter and measure it, you will only find the close to 36v on the furthest terminals (one end positive and one end negative) on ends of the bank.