Each Method account can only ever be linked to one unique QuickBooks file. If you have multiple QuickBooks files, you will need multiple Method accounts.
However you can create a multi-tenancy relationship between different Method accounts, so that you can look at the data from multiple Method accounts together, which would give you the visibility into multiple QuickBooks files from one "Master" Method account (but you would still need a "tenant" Method account for each additional QuickBooks file.) You would need to contact Method to set up the multi-tenancy relationships, and you should be aware that this is a more complicated setup requiring additional customization in Method.
The more important question is why do you have multiple QuickBooks files set up to represent different divisions of your company? You may be able to change the way you do your bookkeeping by bringing all of the data into one QuickBooks file and one Method account, and then using the capabilites of Method to track the separate divisions. Talk to a Method & QuickBooks specialist about your company's needs to see if there is a better alternative for you.
-Mary Longacre