Firstly - I'm honour-bound to point out that ePO 3.6.1 is now end-of-life (but I imagine you already know that )
With regard to MA 4.5, I'm afraid you're out of luck It cannot be controlled by ePO 3.6.1 as there are no NAP files for it - it is strictly for ePO 4 and above.
It also cannot be installed on Win2000 - the installer will report that the OS is not supported.
I was fairly certain that was going to be the case. But, I did need to know all my options.
We are migrating to ePO 4.5 soon. I just have to get a new SQL server (probably SQL 2008) built so I can upgrade my existing database from SQL2000 first. Then, since we've already virtualized our 3.6.1 server, I should be in good shape to upgrade it to 4.5. At least, thats my rudimentary plan.