Charger has selector for flooded lead, agm or gel my trolling batteries are flooded lead, my cranking is agm I can only pick one setting for charger, which one you pick

Usually it's possible to charge each battery separately by connecting directly to their particular posts. Flooded setting if you can manually unplug at 24 hours otherwise overcharges the AGM -shortening it's life. AGM setting if you will leave it plugged in and it has a trickle or maintenance charge function after full charge, it may under charge the flooded by a small amount, losing a little capacity. From readings on battery university.

Pick flooded cell then if you really need your starting battery topped off get a small agm charger.

The only difference between the two is a tenth or two. A flooded cell charger will charge your starting battery to 90%.
If you run your big motor for any length of time when you go fishing it will finish it and charge it all the way up.

Do not charge the AGM in "flooded setting, " during bulk charging "wet cells" the volts range from 14.4- 15 volts .
While the MAX charging volts for an AGM is 14.4-14.7.

https://deepcyclebatterystore.com/do-not-use/battery-charge-settings-agm-vs-flooded-vs-gel/

get a minn kota precision and you can set ea. bank.

https://minnkotamotors.johnsonoutdoors.com/battery-chargers/board-precision-chargers

Battery Type Selection: Each charging bank can be selected to your specific battery type (AGM, gel or flooded lead acid) to guarantee a safe, protected charge