pdirect:How does the Method sync fit into that process?
The process is pretty simple from our end. Method will sync based on the ID numbers from QuickBooks so as long as these don't change durning the upgrade then you'll be fine. Method won't even be aware that anything has changed at all in fact. Specifically for lists like Customers, there is an internal ListID field in QuickBooks. And for transactions like Invoices, there is a TxnID field in QuickBooks.
Just a brief word of caution, in rare situations we've seen bad upgrades where the ListIDs and TxnIDs change. We've only seen this on some of the original QB Enterprise conversions for QuickBooks Canada, and for major version changes in QuickBooks Australia. I don't remember ever seeing problems with the US version.
pdirect: What do I need to do to make sure the Method sync works with v. 12 and doesn't lose data?
There should be no data loss from Method.
~C