The agent needs to provide the course registration info to apply for the visa. If she says you are registered already then you can still take the class, assuming the start date is within a timeframe to get the visa.
On another note, stop trusting lone wolf "agents" unregistered, and unlicensed, to do this job.
after the monthly 65k is transferred from abroad you can remove it from the bank every month if you wish. There are no requirements for leaving it in the bank.
Ditto, more time unless you all want to have the nervous jitters cramps at the same time. Are your Serbian banking documents in English?
Have you read reports here of the Athens embassy success and failure stories or if they are difficult? Make sure your course provider has a strong success rate and that the course is lengthy. Also ensure the start date of the course is well into November.