Very good question.
They talk about how we can manage configuration, start and stop, and add/delete agents from B&R but I do not see how to do that.
You have to edit the agent inside B&R in order to set the application-aware processing... but I cannot edit the agent.
I can only see statistics and disable/delete the agent from the Jobs>Agents menu in B&R console 9.5 Update 1 Version 188.8.131.523.
When you point to a B&R repo, it will change the license back to free and allow B&R to manage the license for you.
So I went back into B&R console, start menu, licenses, and then added my license file.
Then Veeam Agent for Windows now said 'Server' as the edition.
I went back onto that Server and went to configure backup.
Then it displayed application-aware settings as it should.