I have a nice dual bank battery charger. But I just upgraded to a 24 volt trolling motor. Can I split the deep cycle battery charging wires to both batteries and leave the starting battery as is? It may take longer to charge but that's not a concern. Just wondering if it's safe and will they charge OK.

My cranking battery has always been 100% charged when I return from my trip. If your motors alternator is goo, just but the chargers to the TM batteries and carry a portable battery pack.

 

Truth be told, I added an alternator to send the extra charge forward to my TM batteries and they too are often topped off

You can, but I don't really recommend it. I would get a 3 bank personally, but I don't make long runs on my boat to really have much faith in it getting a full charge outta the alternator. 

 

I would say though I would rather charge the two TM batteries with 2 bank charger and keep the cranking by itself w/ the alternator instead of doing what you asked.