I'm not sure I understand exactly what you're doing there, but it doesn't sound right to me.
You need to install the serial numbers through the Backup Exec software itself, either by running the setup program, or through Tools, Serial Numbers and Installation... in BEWS itself.
Choose to add additional options to the local install first, and enter the two serial numbers you have for the two remote servers you want to backup, once this has finished, go through the same again, but this time choose the remote install option, and you will then be able to select the remote servers which you want to install the remote agent to.
I think the problem you were having is that you were trying to install the remote agent software to the remote servers before you had correctly installed the license codes.