we plan to switch to QuickBooks 2016 windows desktop by end of this year. I'd like to know if there is anything we need to take care before switching? We are using QuickBooks 2013 Windows Desktop at this moment. Thanks.
Upgrading your version of QuickBooks and converting your QuickBooks file will not cause any issues with Method.
Just be sure that you are performing an upgrade on the file and not creating a new file and migrating the data. Method will sync based on the ID numbers from QuickBooks so as long as these don't change during the upgrade then you'll be fine.
Wanted to add, it's also best practice to backup the QuickBooks file in the case of anything happening.