Go upstairs in the Pokemon center, then find the lady that says something along the lines of "Welcome to the Pokemon Wireless Club Union Room" (She should be on the top level of the Pokemon center) (On both games) When she asks you if you want to enter, press yes. Once you get both games in the union room, wait a moment, somebody should come into the union room. On one of your games, talk to the other person in the room, ask for a trade. Now, on the game that didn't request the trade, accept the trade. Once you accept the trade, you will be put on the trading screen.
Keep in mind, you can only trade Pokemon that are currently in your party.