What is the best way to merge two companies in Quickbooks?

There is no "best" way, there is only THE way. 

1. Export data from one or both https://quickbooks.intuit.com/community/Help-Articles/How-to-export-your-data/m-p/187949
2. Import data from one or both https://quickbooks.intuit.com/community/Reports-and-accounting/Export-then-import-list-data-into-QuickBooks-Online/m-p/186377

Problems: you can only import list data , if you also want transactions you will have to download bank files and import 

Or find a third party vendor of software with a product to merge