noobie- gel cells are are sealed lead acid batteries and DO NOT like to be fully discharged. I understand what you are trying to do- connect the two in parallel to double your capacity, so the best thing you can do is charge them individually on a good 12V charger before connecting them. This way you'll use the same amount of energy from each then charge them back up to full capacity and they will stay pretty much balanced.
If you want them to last a long time, don't run them all the way down. If you start to see signs of low power, put them on charge immediately.