There are many ways wires can be run to accomplish three way switching, the bottom line is you have a common on each switch usually the common is black or a gold color if you are unsure of which is the common you can use a meter to determine it.
Make sure the power is off and disconnect the wiring from the switch, place the meter on ohms. You should have continuity between the common and one other terminal when the switch is in one position and continuity between the common and the other terminal when the switch is in the other position.
On the common of one of the switches is where you want to connect the hot from your feed supplying power to the circuit. The hot feeding your lights should be connected to the common on the other switch. The other two terminals on the switches are for the travelers, they need to run in between the two switches and each one needs to be connected to the same terminal on each switch.
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