The newest post on /r/piracy gave "go wild posting links and tank this site" vibes.

They probably didn't directly target /r/piracy but blanket hit all subs of a certain size.

Do I need to do anything to interact with both or is that the default behavior?

Did you need to make an account on both or subscribe to both? I see an option to register on the other instance while I'm registered and logged in here.

Will posts on one instance be seen on the other and vice versa or are they completely separate?

That was enough to get me to officially sign up here.