Having MakerWare on your computer will stop you being able to connect with ReplicatorG unless you stop the conveyor. MakerWare connects to your MakerBot via a service called Conveyor. Once you install MakerWare, Conveyor will run in the background and prevent other programs, like ReplicatorG, from connecting to your bot. To reconnect to ReplicatorG, you'll have to stop Conveyor. The easiest way to do this is through the Services menu in MakerWare.
Now make sure your computer is connected to your MakerBot with the supplied USB cable.
Open ReplicatorG by double-clicking the application. The ReplicatorG software will try to connect to your bot. You’ll see the band just below the buttons turn light green if everything goes OK.
If your machine doesn’t connect properly, go to the Machine->Machine Type (Driver) menu in ReplicatorG and choose your configuration. A dual extrusion Replicator would be "The Replicator Dual." A Replicator 2 would be "Replicator 2."
Next go to the Machine->Connection (Serial Port) menu. On Windows, try selecting the highest-numbered port. Then click the "Connect" button.