My boat came w/ two bilge pumps. One is a Rule self contained automatic and the other one is a manual. They were wired in a way so that they both worked automatically and I could also manually turn them both on at once. A mechanic cut the wires because the automatic one wouldn't turn off and now I can't figure out how they were wired. The auto has black, brown, and brown/white wires while the manual only has black and brown. I have black, brown, and brown/white wires already run to that compartment. I am hoping that one of the local wiring gurus can tell me how to wire them back how they were. I have tried several options and haven't had any luck yet.

Just my opinion, but I'd lose the automatic pump. They are problematic due to the condition you already have - a piece of trash getting caught under the float in the automatic, and it will stay on until your battery is dead. I've run several boats now with only a manually operated pump, and you'll know when you need to turn it on. If you do that, it is very easy to test the wires with a volt meter to find which 2 correspond to the manual switch - never look back.

Rule #1. The most important things on a boat are the bilge pump. Try it after launching every trip. When you need it you really need it. This can avoid an involuntary bowel movement.
Manual and if you have two have em wired to two different sources, just in case. You also need two.

I keep my boat plugged in when it is parked so I'm not worried about my batteries dying. I really liked the way my pumps would automatically come on when needed. It was helpful when I would leave my boat docked overnight. I am just trying to wire them back how they were without having to buy another automatic pump.

Nobody knows how to wire them?

The brown/white wire is the "auto" wire. It should go to the auto side of the switch. It will also splice into, or connect to the brown wire of the other pump. It's possible with a 6post switch this jump was made at the switch. Another way would be if the two browns connect either through a junction or the switch, but the brown/white would need to be connected to the auto side of the switch.
John