Basically figure out what the "normal" kV of your charger is, and if it is not up to snuff push the "A" button (for amps rather than kvolts) on the fault finder and start at the charger. 

A fence charger normally puts out a lot of volts on each pulse but not many amps - unless there is something touching the wire and providing a route to ground.

This time of year you will see some current, maybe 1 or 2 amps,  going to almost every branch due to green vegetation growing up and in contact with the hot wire.

If you have a real fault such as caused by a tree or branch falling on the wire and putting it in contact with the ground or a bad insulator or tangled hot and cold wires, you will see significant current amps (often 5, 10 or 15 amps depending on the size of your charger) flowing to that point.

What the fault finder does is to let you follow the amps to the problem spot.  For example if your charger connects to the fence in the middle somewhere, press the A and hold it up to the wire on either side of the connection.  The arrow will show much higher current flow to the branch with the fault. Then walk down this wire, periodically checking amps and direction again, until you get to the next junction or the fault itself.

If you go past the fault the current shown on the meter will drop off so you know you went past it. Go back to the fault or branch.

Just think of amps as water flow in a pipe. The pipe has a leak (the "fault") where water is flowing out (to ground).  The meter is just showing you the direction and magnitude of the flow of water in the pipe. Following this flow should take you to the leak/fault.

Good luck.

Jim