Yes! To build dependencies between models, you need to use the ref function. The ref function only takes one argument — the model name (i.e. the filename). As a result, these model names need to be unique, even if they are in distinct folders.
Often, this question comes up because users want to give two models the same name in their warehouse, splitting them across separate schemas (e.g. stripe.users and app.users). Checkout the docs on custom aliases and custom schemas to achieve this.