Hi Sixtel,
The Customer table is the table that links to QB. It is really a subset of the Entity table, which is the QB table that contains all of Customer, Vendor, Employee and Other Namess. The Contacts table is a Method table. It includes all of the Entity table names (as fullnames) as well as the additional contacts associated with them.
Method has some info on this in their "help" files. There may even be a video. It can get confusing.
One way to understand the relationships is to export your customer table and the contacts table. With your data is should be easier to see the relationships.
Hope that helps.