You did not share the entity configuration or tell us what kind of application you're building. In a typical application flow one of the entities is selected in the user interface (UI). For example, the Project is selected in the UI. The UI shows all the employees in the project with an option to add an employee to the selected project. This assumes the Project entity has collection of Employees property. From there it's a simply matter of adding the an employee to the collection of employees and saving the entity.
I think you'll be interested in reading the EF many-to-many relationship documentation.
Also, the official ASP.NET Core data tutorials have a many-to-many relationship example with common programming patterns.
Razor Pages with Entity Framework Core in ASP.NET Core - Tutorial 1 of 8