installing a replacement fixture with three lamps in one on a two way switch
In most modern fixtures that have multiple lamps, the wires are preconfigured going into the hood so that there is only one black (hot), one white (neutral) and one green or bare (ground) wire coming from the fixture to be attached to the wires in the box.

If there are separate wires for the three lamps, all three black wires should be twisted together and connected to the single black wire from the box, capped with a wire nut (and taped if you want added protection). Similarly, all three white wires should be combined with the white wire from the box. And finally all the green/bare wires combined with the ground wire from the box.

The switch wires are already worked into the overall wiring (assuming they were working before) and need not be modified. By the way, when a lamp is controlled from two locations, the switches that control the lamp are called three-way switches.