The Voltage will drop 12with the system running due to the current draw from the pump, Voltage will also drop down the length of the cable, Copper wire does have a small resistance vale to electrical current so the long the cable the greater the volt drop down its length. Poor connections will also have an effect.
On the charging capacity via a relay
Remember the controller is not able to generate electrical current.
The maximum rate we can charge is set not by the controller as it acts only as a switch once the alternator/engine are running, but by the capacity of the alternator. The charging capacity is controlled by the alternator which is generating current.
The amp per hour charge rate is dependant on a number of factors for example the length of time the engine/alternator are running and how quickly they run.
Most alternators are designed to trickle charge a battery so the longer and faster they run the higher the charge rate. (Up to the maximum capacity of the alternator and battery) There is also a restriction based on the maximum capacity of the alternator and battery in any system plus any drop off through the wiring due to resistance.
The ampage per hour rate will drop off as the battery nears full charge, the batteries capacity to take amps drops as the voltage capacity nears its maximum. The only way of physically pushing higher current into the battery would be to increase the Voltage capacity and increase the maximum generating capacity of the Alternator.
for the technically minded there is Ohms Law
http://en.wikipedia.org/wiki/Ohm%27s_lawCheers
IAN