The short/drain is a huge factor, when one cell discharges less then the others, the others have to pick up the slack and result in a lower over all voltage discharge. If you have two batteries in parellel you'll hurt what wouldbe a good battery and if I'm correct when running in parrel, you maintain the original voltage, but increase /decrease the amp load. OHMS law.
I bought a small breaker board for 12vdc and installed it on my 14ft alum. I then just rigged the troling motor to that with a battery switch over. Works great and when I run my depth finder I don't have to worry about battery drain, The whole setup cost less than 5 bucks...batteries were obviously more.