Two parallel batteries will last twice as long a single battery.
Not being nit-picky, but just providing information. 2 parallel batteries will last "marginally" longer than 2 separate batteries drained individually. The slower a battery is discharged, the more AH it can deliver. I wouldn't expect a "LOT" more run time of the trolling motor, but it can provide more run time than draining the batteries individually.
Of course then comes the problem of running parallel batteries, as they will stabilize to the weakest battery (which could equal running them individually). And, 1 bad parallel battery can ruin the other, and ruin a fishing trip...
I have a battery switch on my jon boat, so I can run the TM batteries parallel, or single. If the batts are new or in the same condition I'll run them parallel. If I know one of the batteries is weak, I run them separate.