How do you design an app

Hello IHs, I have been here for a while and I have watched lot of great project. I am trying to develop a Student Information System with Django, and I wonder:
How do you design your app?
I am not talking only about tools for UI design. I mean, make a full app involves UI, UX, user flow and lot of thing. Last days I have been learning about agile methodologies for development apps and I don't know how a indie hacker faces all this parts of development.
Do you use diagrams, tool for UX, etc? How do you start when have an idea?
Thanks for all your replies.