Red to red. Black to black. One of the brown goes to ground(it has an o-ring) and the other to the bare wire on your pump cable.
If you have an old system that did not use a weather pack 3 prong connector, call me for the female end so it clicks to the male end on the pump.
This way in the future.. you wont have to go through this.
You should have recieved an upgrade module as well.. that ties in with all of this.
Pumps earlier than '05 were soldered directly and had no weatherpack plugs.