How do you connect Profit Calc with multiple Shopify stores?

Yes, it can! To use Profit Calc with multiple stores, each store would have to have Profit Calc installed. Each store would need its own subscription as each store would need its own setup (e.g. access token, product database, order database, ads login/connections, API access).

There is a new setting to link your multiple stores together, so it can be done automatically using email confirmations. This can be done on this page here.

Also to note with the multiple store settings:

Each store can be selected individually or viewed together under "All Stores" under the Analytics sections. 

The currently logged in-store is displayed in the top left of the sidebar menu. The settings will only show for this store. To change stores, select another one using the selector in the top left.