Main Index Template (index.php)

I am trying to create a custom home page that goes beyond going into the “Reader” settings. The navigation bar for this site sits on the top on all pages except the home page, in which it will sit on the bottom. What is the best way to achieve this?
How do I use the “Main Index Template (index.php)” in the Editor? I see how to edit the page, but how do you set it as the home page???

https://www.thesecretcity.org/

https://www.thesecretcity.org/wordpress/?page_id=2

Any help is appreciated. Thanks