If you are using the CLI,
When you have a solution with 2 projects API/WebApp and a DataAcess project you can pass in the options on the command line.
My_Solution
|DataAccess_Project
|-- DbContext.cs
|WebApp_Project
|-- Startup.cs
Change into the solution directory
CD My_Solution
dotnet ef migrations add InitialCreate --project DataAccess_Project --startup-project WebApp_Project
dotnet ef database update --project DataAccess_Project --startup-project WebApp_Project