Count 22 for Angela Wagner applies from Jan 1, 2016 to November 12, 2018. That's well before the murders and right up to the day they were all arrested. It includes all the W's and Rita Newcomb, John Doe and any other unidentified or unknown individuals, the latter being a "catch-all" description that allows them to include other participants they may later discover.
The pattern of corrupt activity includes: Aggravated Murder, Aggravated Burglary, Unlawful Possession of a Dangerous Ordnance, Tampering with Evidence and Obstructing Justice, plus everything in Counts 1 thru 21. The indictment uses the qualifier and/or for these activities, meaning some could be guilty of one or all of these.
IANAL, but John Doe could be (1) a person they haven't yet identified, but know was involved in planning and executing these offenses or (2) a confidential source who participated in some of the planning, etc. and helped LE by recording or relating what was said in some of their "planning meetings".
The indictments mention John Doe because he will probably be part of the trials in some way, either via witness testimony, affadavit, etc. If he's a real person and known to LE, it could be someone who cut a deal with prosecutors and whose identity they want to protect for now.
I'm probably wrong on this, but its the best I can come up with.