I've been using Zencart for years, and have never written a line of PHP - wouldn't know how.

Changing the index page (assuming you mean changing the content) is done by editing define_main_page.php and inserting HTML. You can do that with the Define Pages Editor in Admin - Tools, or manually.

Sideboxes are turned on or off in Admin - Tools - Layout Boxes Controller. If all your boxes are set to 'off', you probably dind't reset them (Layout Boxes Controller - Reset at the bottom) after you changed templates.

I'm not sure what you mean by a 'navigation menu'. Zencart has a bunch of those built in, and there are variants available in the mods (Free Software Add Ons, above).

Most actual design changes atre done in the stylesheet(s).

No 'wrath' here BTW. We usually refer newcomers to the Tutorials/FAQ because most people don't check them first.