You have probably not done anything wrong as long as you haven't tampered with files inside the 'root/concrete/' directory. If you want to change core functionality you should do an override.

Please see this how-to to find out more about overrides:
http://www.concrete5.org/documentation/how-tos/developers/change-th...

A good how-to on custom templates can be found here:
http://www.concrete5.org/documentation/how-tos/designers/change-how...

And a how to modify a core or packaged theme can be found in these:
http://www.concrete5.org/documentation/how-tos/editors/customize-a-...
http://www.concrete5.org/documentation/how-tos/designers/modify-a-p...

When it comes to breadcrumb template there is a known bug in the 5.6+ versions which I have added a small fix for: http://www.concrete5.org/developers/bugs/5-6-0-2/core-auto-nav-brea...

Whenever you do changes in the source files you should turn off all cache from the dashboard, and it might also be a good idea to clear your site cache (search for 'clear cache' in Intelligent Search in the edit bar) now and then. And also to clear your browser cache so you know will be presented with your latest changes.

Oh! I nearly forgot to mention this excellent theme development how-to which explains all steps in creating your own theme: http://www.concrete5.org/documentation/how-tos/designers/making-a-t...

I know there are loads of links in this post, but they do explain things better and in more detail than I would possibly manage to fit in here (and why invent the wheel again?).

Thank you very much, all useful info. I'm slowly learning coding by groping around the site,

I found some of the issue; it was in the theme's header.php. I had moved the Header Nav area out of the headerright div and into the header div. It seems that if Header Nav is in any div besides headerright, the custom templates don't apply. The client would like the Auto-Nav below his header logo, the whole width of the page. Any input? Thanks!