Charging boat batteries in parallel

Hey guys, I am wanting to charge my trolling motor batteries. I have 2 12 Volt batteries in parallel. I have a charger and was wondering how to charge the batteries do I just charge one side at a time? Whatever I have been doing has not been working because my batteries will be totally drained after I put them on the charger. Have any of you had this experience before and know how to fix this? Thanks!