So you have the box at the top, this confuses our users, so we need to remove it. To do this you can just use a simple script on the front page.
1. Edit the front page and add the “Script Editor” web part.

2. Give it a suitable name, and then enter the following snippet:
<style type="text/css">
#titleAreaBox #SearchBox {display: none !important;}
</style>
3. Save this web part and the page, and refresh, you’ll see that the search box from the top has disappeared.