Tim; I'm assuming that since there's been no mention of a custom control layout, you mostly likely have Series I electronics.
The switch on the lower horn is the pickup selector switch; the choices are neck pickup, both pickups, bridge pickup and standby. Then for each pickup you have a volume, low pass filter, and Q switch. If something doesn't seem right when using the 1/4 jack, it may be that the jack is stereo, and by using a regular mono plug you are only getting one pickup.
For further info, check the
FAQ.