Amps are amps and it will run a trolling motor... The problem is the plates in a starting battery are thinner (thin to give up amps fast for starting) then in a deep cycle and can/will warp and kill the battery. You will want to look and see how many Amp Hours the battery has to give you a idea of how long it will run your trolling motor. Good luck!
50 for that case, I have one of those cases, they work fine, but you can get them a lot cheaper.