The jumpers go underneath of the stepper drivers to set microstepping drv8825 drivers all three pins jumpered results in 1:32 microstepping.
Make sure that the silkscreen on the stepper drivers match that of the megatronics.
As for the extruder fans: If you would like it to be on all the time hook it up to the 12v line from power supply. If you want to be able to turn it on and off, or set speed you should hook it up to fan 1 which appears to be under the extruder stepper. See picturr
wiring
Prusa i3 Rework - Ramps 1.4 - E3d Lite6 - Full Graphic LCD Controller