Is there a switch to charge single batteries in a series array?
Generally, it's a Bad Idea to put batteries in different states of charge in a series/parallel battery pack, which is basically what you're proposing. You really want to have all the batteries in your pack at the same state of charge at all times.

What you really need here is a charge controller (basically a DC-to-DC boost converter) that takes whatever voltage is available at the output of the generator and converts it to the bus voltage of your battery pack.