On a 2-way wager, you'll win regardless of the method of your team's victory (in regulation, overtime, or after a shootout). A win's a win. With a 3-way wager, your team must win in 60 minutes - an overtime or shootout win for your team will still lose you your bet.
3 way means that there are three possible conclusions to the bet. Over the corner amount. Exactly the corner amount. Under the corner amount. Same as with Win/Draw/Lose, you have to get the corner amount right or you will lose your bet.