Hi Sawyer,
Francois beat me to it for most of this but here's what I was writing, a little extra info.
(1) Yes, the Managed System Setup Auto configuration, byte code instrumentation step will connect the DAA on your managed Java system to SolMan and Wily Introscope.
(2) The excellent Diagnostics Agent Installation Strategy guide attached to note 1365123 on page 23 shows that the host agent has been auto-installed since Diag Agent 7.20. Read this document, it has very good info on the agents.
(3) I have been connecting and monitoring Java systems in Wily for a long time. I don't think they ever didn't.
Welcome to SolMan and good luck,
David