I have been assembling shunt boards for power switching this week from inexpensive kits I bought at a local electronics store. I'm going to finish Sparkgap in the next few months the way things are going and this is the first electrical system that will be installed for power management.
My original battery setup had your standard car charger hooked up to panels aboveground. There is supposed to be battery protection built into the batteries I bought but it did not work correctly. A couple months of discharge cycles and both my expensive camping battery boxes were completely shot.
You have to connect true power shunting boards to fully disconnect your battery when it reaches a level you will set according to whatever constitutes optimum cycling for your setup. Once disconnected, particularly from a wind generator, you have got to shunt that power into a load, be it an exhaust fan, lighting or a heater. You need something that can handle the maximum power input of your generation system without burning out.
The best way to intelligently charge an array of 12 volts is to connect shunt boards in parallel, so each one switches to the next battery in line until it gets to the end and then activates the load when all batteries are fully charged. If you make good use of the load you can use that excess energy to do things like run the water filter, run the exhaust fans, run hydroponics pumps, etc. depending on what the most energy hungry application is in your shelter.
The greatest thing about shunt boards is that they are built from a handful of cheap, hardy components and they have some built-in resistance to EMP. Even so, I am considering using a mechanical cable as a drive train from the vertical axis wind turbine down into Sparkgap for turning the motor so that I can do my maintenance belowground and also avoid long runs of wire from topside. This is actually much easier than it sounds - I have tried running a piece of braided cable inside a nylon sheath up to ten meters away connected to a motor and the torque generated at that distance is more than sufficent to turn a 12 volt DC generator shaft.