It uses client/server to connect. Once you load the rom you want to play, the netplay option in File becomes available. In it, someone acts as the server, and hosts the game, and the other person acts as a client, and enters the host's IP to connect. Have the host visit a site like whatismyip.com or ipchicken.com to find out his IP. You may have to open the port in your router (and your friend's as well) if you cannot connect. Default port is 10000 but it should let you change it if necessary.

If you find it hard to connect, or once connected, feel unsatisfied with the quality of the connection, you could always just use one of the many other NES emulators with netplay, such as Nestopia or JNes.