Hello Greg… Thank you for posting this in the forum. I believe I have a similar need. I have a public facing site which can be managed via a single RapidWeaver project but where things get tricky is the membership side. The dashboard pages would live in the main site project while all the content sections would all be individual site projects.
What this requires is that the public facing pages all need one type of header (Nav) and footer while the dashboard pages and individual member content sections, which are designed and published via separate RapidWeaver projects, need second layout for their headers (Nav) and footers.
The goal is to be able to publish any changes to the headers (Nav) and footers from one place. Further the membership content RW Projects would be just that, each content RW Project would simply manage its content and pull the header and footer in via the PHP Include approach. I am curious how you got on with things and if you wouldn’t mind elaborating further?