Hi mlwells,
If you're going to use a different QuickBooks file then you will need to create a new Method account. In order to keep your data you would need to either re-enter it in your new account, or export it from your current account then import it into your new account, however this won't be easy as it is a flat file import process. Customization won't go to waste as you can copy over screens from one account to another but this should only be done across the same account type, i.e. QuickBooks Online to QuickBooks Online, not QuickBooks Online to QuickBooks Desktop or vice versa. So if you're currently using Method for QuickBooks Online make sure your new account is also a Method for QuickBooks Online account.
When screens are copied from one account to another, the tables that are associated with those screens are copied over as well, if needed, but the data held within those tables is not copied over by default. For instance, if you have a custom dropdown field in the Invoice table and you create a new table to hold the selectable options within this dropdown list, when copying over the Invoice screen only the table gets copied over to the new account but not the actual selectable options within the dropdown list. So before you start copying over anything ensure that you check which custom dropdown tables you would need and enable the Copy table values when this table is copied during a Copy / Import Screen option. This can be found by going to Customize > Tables/Fields > then by clicking the Edit Table... link next to the appropriate table.
- Ashur