Not sure I understand the question entirely but as I understand it Method was built like Quickbooks was built. Entity and Contact are not separate things. The primary contact is a field within the record for an entity. Method doea add the ability to add in additional contacts but that doesn't really change anything.
For jobs, jobs are just sub-customers in Quickbooks. if you end up with many jobs for the same entity that also have the same primary contact you will have that person listed over and over again in your Method contacts.