Think of the available module positions as a big sliding puzzle. When a position is not filled (no module assigned to it), then all the other pieces of the puzzle slide in to fill the gaps. In other words, you can make each page as empty or as filled as you wish.
There is a special option only for the Homepage (you can set this option in the Aqua3 template options), where you can hide the main Joomla content (articles, blogs, etc.). So if you want, you could just have only one module published on your home page (like a hero unit with an image slider) and nothing else.
When the viewport (screen size) becomes smaller, the top menu, top search and sidebar modules move to below the main content (easier to read on smaller screens like smartphones and tablets). First the sidebar modules become 2 columns below the content, and then 1 column on even smaller screen widths. The above, bottom and footer modules also adapt their column behaviour.
You can test the results by resizing your browser window width or by zooming the page (Ctrl with +).