This should give you the basic idea.You don't happen to have a pic of exactly how this is set up do you?
I've never done electric wire, so seeing it would really help.
Note how the "hot " wire goes from the charger to the TOP wire of the fence, and then it uses "jumpers' to connect the lower wires;
All you have to do is wire in cut off switches in the jumpers, so you can turn off the lower wires but leave the upper wires on

http://www.afence.com/Electric_Fence/how_to_elecfence/elecinstall.htm
Typical cut off switch:
http://www.premier1supplies.com/detail.php?prod_id=419