main.qml contains the PageStackWindow window (see docs, but it's the container, dealing with menus, status bar, rotation, and the stack of pages).
MainPage.qml contains a Page object, which is the actual content that is being displayed.

If your app is single page, then you edit in MainPage.qml . If you want multiple pages (that sliding effect when opening a new "window"), you'd add the new Page into a new .qml file, and reference it in main.qml.