You pay once
You will pay while you submit your application, with CC or electronic cheque. The fee is $175 I believe. They will give you a receipt number (MSC series) and tell you to call NCSC for a 'biometrics appointment'.
At the ASC they will print your index finger and take a picture, there is no payment involved at the ASC.
The EAD biometrics is different from the I485 related fingerprinting (and probably different from the biometrics for the actual GC.)