If I have two 12V 50 AH Lithium batteries connected in series to power a 24 V trolling motor, how would I connect the 12V on- board charger connections to charge both batteries simultaneously?

As long as you have a lithium charger , nothing changes as you hook up the batteries .

Have at least a two bank charger and connect a bank to each battery, same as any other batteries.

Some chargers will charge lithium and wet cells , AGM at the same time .

Ebay has some ionic battery chargers , 3 bank is $50.00 , 4 bank is $75.00

Thanks y'all.

noco genius and minnkota pc chargers will do lithium, my pc does it in agm mode

Well my cheaper Ionic Lithium refub trolling battery took a dump , gamble is i think i lost . Was down to 49 % and about 10min it shut down , no bluetooth . No nothing.
Short story when i got it was reading 12 v 48 ah , so i called cust service , they said to drop it down to 20% , and it would fix it . So it on the charger and it was reading 1% 46 ah , 13 cycles , 4 hrs to charge
Had to come in after a hour

Checked Refub Ionic battery this morning and it read 100% 12 v 46 ah , so i loss 2 more ah . So that was a waste of $ 175 .00 ,
only used it twice , 30 day warranty , now i don't have any warranty they should have junked this one ,

I'd do a capacity test on it. The apps aren't always the most accurate and have been an on-going challenge across most brands.

4 hours of use and it quit's completely , dead as a dumb bell .

Sounds like you have a bad cell in there or the bms is not working.

Running what device?

Trolling motor

Easy equation.

Amp hour capacity of battery divided by max amp draw of the unit your powering = Run time.

Example

Two 100 AH 12V batteries in series = 200 AH divided by (say a trolling motor with 50 AH max draw) = a run time of 4 hours.

If you're running the trolling at half speed setting then that would be a 25 AH draw and you'd get 8 hours run time.