i had in touch with migration agent, what he did is email the nsw.pese and just said to wait for the reply from them though. I thought there should be another way to pay for the fee?
Your migration agent should know all this and be able to explain it to you. I do not understand why people pay money to professional registered migration agents and then need to go on a public forum to get answers to their questions.
If the agent has followed correct procedures, then I think you should not be second-guessing their actions. if they haven't, you should take it up with them and ask them what the procedures and payment options are and how they have addressed the issue.
2.8 A registered migration agent must:
(a) within a reasonable time after agreeing to represent a client, confirm the client's instructions in
writing to the client; and
(b) act in accordance with the client's instructions; and
(c)
keep the client fully informed in writing of the progress of each case or application that the agent undertakes for the client;
2.20 A registered migration agent must:
(a)
find out the correct amount of any visa application charge and all other fees or charges required
to be paid for a client's visa application under the Migration Act or the Migration Regulations; and
(b) give the client written advice of the amount of each fee and charge; and
(c) if the agent is to pay an amount for the client - give the client written advice of the date by which the amount must be given to the agent so that the interests of the client are not prejudiced; and
(d)
give the client a written notice of each amount paid by the agent for the client
https://www.mara.gov.au/media/553229/Code_of_Conduct_April_2017.pdf