I haven't seen much released about the Encounter Libraries, so I think a lot of your questions are still unanswered. I am assuming (hoping, as I own quite a few myself) that those, like all the other purchased content, will be available in HLO once they're released.
So for now, if you want to use it to run a campaign, you'd need to manually create those encounters. That's what those of us using Campaign Theater for PF2 have been doing since it was released.
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