Short answer: there isn't currently a way to keep auto-sync switched on while excluding specific entities, such as your own firm or entity group. Auto-sync applies the same rule to every meeting.
How auto-sync decides where to file
Auto-sync decides where to file a meeting based on the email addresses of the attendees. If the attendees on an internal catch-up match your own firm's entities, auto-sync will file the meeting against those entities, because that's what the attendee emails point to. There is no per-entity "exclude from auto-sync" setting today.
Workaround: use Manual Sync for internal meetings
If you want auto-sync for client meetings but full control over where internal meetings go, use Manual Sync. With Manual Sync you choose exactly where each meeting is filed, so internal meetings only sync when and where you decide.
Karbon: see Karbon Manual Sync in Vinyl.
FYI: use manual sync to place each meeting against the correct client rather than relying on attendee matching.
Want per-entity control in auto-sync?
Excluding specific entities while keeping auto-sync on is a feature our team is aware of. If it would help your workflow, let us know in the chat below so we can factor it into future updates.