In the Square App Integration: How do I get the imported Square transactions to: - show/track GST - add the transaction fee Square charges to the expenses

You should have a 3rd party connector app to reconcile Square transactions into QBO.

Hi there. I'll be happy to provide the info you need so you can move forward with your work. In order for the tax to show up on the transactions, you'll have to set up your taxes in QuickBooks and manually assign the tax codes to the missing transactions. Have you already set up your taxes?