It will not be enough. Your boats alternator only puts out roughly 14 A at 3500 rpm, I verified this using a Victron smart shunt on my boat. You are going to need an AC type charger to charge your trolling motor batteries. Here’s the good news, LiFePO4 batteries can charge very quickly, if you have 100Ah batteries they will charge in roughly four hours from an 80% discharge as long as you use a charger capable of that charge rate. I run Victron Energy IP67 chargers and they charge at 25A, I’ll be swapping out my remaining MinnKota battery charger that currently charges my start and house batteries to a set of Victron IP 67’s over the winter.
Check out this thread I posted on LiFePO4 batteries.
https://jetboaters.net/threads/conversion-to-lifepo-batteries.35834/
It was a much longer journey than I thought it would be! There is some great input in that thread from other members. In my opinion Battle Born batteries are the best bang for the buck.
Along with the trolling motor batteries I also upgraded my house battery to a LiFePO4 battery which is a great pairing with the charging system on our boats. Upgrading the house battery requires modifying the BEP DVSR to either an ignition hot or storage mode, the latter of which is what I use, these are variations that BEP has documented in their literature.
You will also want to install a Victron smart shunt on your trolling motor battery bank to keep track of the state of charge. I’ve installed two, one on the troller and another on the house bank. Not having these on your batteries is just guessing at usage and state of charge.