I recently purchased a 24v trolling motor. Can I charge the batteries with my 12v charger while they are still wired in series, or do I need to disconnect them and charge each battery seperately?

Yes, charge them separately without disconnecting them, current will only flow between the positive and negative of the charger/battery connection. Lots of people use multi-bank charges that are mounted in their boats and each bank is independent of the other.

You should get another charger and charge them both at the same time. For longer battery life the battery should be charged as soon as possible after a discharge.

Thanks for the information. The 2 batteries are different brands and different amp hrs., both are 12v.. Is that going to cause a problem with the trolling motor? I would rather not have to buy 2 new batteries, if I don't have to.

Different batteries work fine. Your total run time will be the determined by the lowest capacity battery.

Thank again, you have been very helpfull! I am going out this weekend and try out the new motor.

It is generally important to match batteries that are used in series.  This doesn't mean it won't work but if they are different capacity and one battery runs down before the other, the good one will try to force current through the dead one and damage it.  When they are matched, they both run down together and there is much less risk of one damaging the other.

So while it will work, be very alert to loss of power and stop using them well before the weaker one is discharged.