Yes! Just add each Shopify store as a sales channel within Trunk. To do so, choose the store from within Shopify first:

Then, go back to your Trunk account, and click Sales channels from within the top menu bar, then hit the Add button, and select Shopify.

Once you select Connect account, you will be redirected to the Shopify App Store, from which you'll have the option to install the app and add it to your Trunk account as a second sales channel.

You can differentiate between your Shopify sales channels by hovering over their quantities.