Does my AE/AO DM still work ?

MYOB AE/AO Document Manager will continue to work but with limited functionality. Historical documents and templates will be avaiable normally, but new documents and templates can only be created in Nimbus Document Manager. Learn more about AE/AO Document Manager changes.

How does MYOB AE/AO know my practice is using Nimbus?

There are 5 new fields in the AE/AO database Configuration table.
When the NimbusPracticeId field has a value in it, then this will identify your practice as using Nimbus

These will have been setup when you first installed the Nimbus Profiler. See here on how to do that:
https://nimbusportals.atlassian.net/wiki/x/FQDny

How can I set the Custom Fields for a document?

Once the document has been saved into Nimbus, you can then modify the custom fields from within the document using Nimbus Custom Fields.