Your main folder IS the top level folder.
As you described it, you have your folder structure like this : main folder>vault>inbox/notes/templates
You don’t need to create another folder, just use your main folder as a vault in the iOS app, and you’ll have everything under one vault like on desktop.
If this doesn’t work, then it’s not the normal behavior, and you need to report it in the mobile section.
Also, it should recognize the sub folders automatically.