Hi VLocke,
As long as you are creating the table and fields from within Method, you shouldn't have to worry about this new table (let's call it "Customer2") syncing with QuickBooks. Method isn't able to create fields/tables and have them sent to QuickBooks. The only time this is even remotely possible is using Custom Fields, however custom fields have to be created in QuickBooks anyways, then they sync over to Method.
-Ben