New boat came with a promariner pro sport hd 20 plus on board 3 bank charger. Trolling batteries are AGM. Starting battery is flooded cell. Charger had a setting for Flooded/AGM/Lithium. Do I need to get an agm starting battery or will one of the settings work for both? Obviously not lithium setting.

Why would you not just use the flooded setting on the charger? If it doesn't give you the option I would assume the charger knows how to detect which is which. I've had chargers that will do so.

He has a three bank charger.
Two of the banks are connected to two AGM trolling motor batteries.
One of the banks is connected to one liquid lead acid cranking/starting battery.
With his brand of on board charger, you manually select what type of battery the charger charges.

The charger charges all three banks at the same setting at one time.

My bigger concern would be how are you going to run four graphs, 360, talons, lights, livewells and start your engine off one battery.

I say buy a fourth separate l small AGM to run graphs and hook it up to the three bank charger in the AGM setting.
This will minimize interference.

Then purchase a cheap Viking 4amp portable charger from Harbor Freight to charge the old school liquid cranking battery when he gets home.

2 AGMs for TM
1 smaller AGM for graphs
1 old school lead acid for cranking/starting/bilge/lights/horn/livewell/talons.

One onboard three bank charger for the AGMs
One cheap 4amp portable 12V charger for the old school lead acid cranking/starting/bilge/lights/horn/livewell/talons.

I dont have room for a 4th battery.

They make small AGMs for PWCs like jet skis that can fit in almost any compartment.
They have enough amp hours to run graphs all day no problem

That’s kinda how mine is setup. But I have the motor battery for the motor only. Two group 31 for the trolling motor. And a group 27 on live wells, lights, stereo, graphs…everything else. I have a three bank on the troller and house batteries and a single on the motor battery. Every time I get home I plug in the chargers and the motor battery charger displays the starting battery as fully charged in about 30 seconds. I feel like I could just not even have it on a charger, but I have a single bank 15amp and it’s would just sit in the garage if it wasn’t in the boat.

This

I would buy a charger that you can set ea. bank to type of battery, you don't want to charge agm on flooded setting and vice versa.
minn kota precision or a noco genius

I run an AGM for cranking and graphs etc. I run 2 lead acid batteries (for now) for TM. I charge my lead acid batteries with the onboard charger and use a stand alone for the AGM.

What boat is it? What motor? What electronics? Then we can help you