Tom.
Try with the lights on, that way you can see if it's charging, if the ammeter is working that is, that way you will see a discharge with the lights on but it should come up to a charge reading when you rev the bike, your quite correct the square rectifier is under the seat with three wires, four connections.
If you have recently fitted a new alternator make sure you have clearance between that & the rotor, many folks have burnt out alternators by not checking this.
TTJohn