Hooking multi-cell batteries directly in parallel, such as car batteries, deep-discharge, etc., is not healthy for the batteries. If one begins to develop a weak cell, it will continually pull current from the good battery, eventually damaging it also.
Here is a good explanation:
Battery Isolation This is done all the time in RVs, boats, golf carts, etc. The diodes are regularly available at boat or RV service centers.
