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EPW, ADPW and and Exchange Resource Forest

Hello all-
I'm needing some clarification here regarding these utilities and when to run them.
I've consulted the documentation and read this KB article:
Here is the environment:
* User accounts reside in Forest A
* Exchange 2013 Org in Forest B. All user accounts are disabled
* Target is 2016 AD and Exchange, single forest-when-migrating-account
* Customer had all accounts created in the target so we are matching source/target objects
* Also, we have about 3000 users that already log into the target but have their mailboxes in the ERF
From what I'm reading, I'll need to run both ADPW and EPW but at different times. The article states "In the above scenario ADPW (Active Directory Processing Wizard) needs to run on the resource Exchange forest A after all AD accounts from domain B are migrated to domain C" so the AEA is set in the ERF to now point to target Exchange. Is this done when ALL mailboxes have been switched to the target? Or do I run this as I switch mailboxes?
Is it the same using ADPW?
How do I control which accounts get processed? I don't see an INI option for ADPW and it's greyed out for EPW even though it exists.
Sorry for the length of this but I wanted to be as thorough as possible.