Yes, you can switch inventory master settings between Shopify and QuickBooks and vice-versa even after you freeze it while configuring your Pipemonk account settings for the first time.
1) To see, how to set QuickBooks Online as you 'Inventory Master', click here.
2) To see, how to set Shopify as you 'Inventory Master', click here.
Note: We recommend you to set "QuickBooks Online" as inventory master while configuring your Pipemonk account settings. It helps you in getting right reports (i.e.- COGS and Profit & loss) which are important to your business.