Yes, voltage drop is another very important aspect to designing a dual battery system. Again, that's why I would recommend 50mm2 (or AWG 0) cable between your starter and aux batteries. For example, a quick calculation gives a voltage drop of less than .2V over a distance of 7m with current 50amp based on 50mm2. So if your alt produces 14.5V nominal, 14.3V at your aux battery is good charge voltage.
Anything less than 14V will be a waste of time, and you'll never be happy with it.
There is a calculater here;
http://www.calculator.net/voltage-dr...s=80&x=36&y=16