Do I have to include all individual and multi-occupant spaces and do they have to be consistent across IEQc6.1 and IEQc6.2?

In short, yes. If IEQc6.1 and IEQc6.2 are both pursued then all individual and multi-occupant spaces must be included. LEED reviewers will want to see consistency across these for IEQc6.1 and IEQc6.2.