You can set your locations up in Shopify and specify the inventory in each. Can you send through an example of what is occurring now and how you would prefer to manage it?
Depending on your complexity you could start using an ERP or inventory management system or just have some custom data flows.
You can take a look at ConnectPOS! As a leading POS solution, we've supported multiple brands to connect their online and offline stores. I know that our app will be perfect to solve your problem!
You can assign each location to an outlet on ConnectPOS, and that assigned outlet will only show the inventory within that location. There will be absolutely no mixed data. If you want to manage the other location, just simply switch between two outlets. Every task can perform in-app.
More than that, ConnectPOS also supports real-time synchronization between POS and online stores, so you don't have to worry about missing any changes.