A couple months ago, I fooled around a bit with the advanced layout options when I made our site. Now, when I try to do things from the admin menu nothing changes. I'm not sure if this has anything to do with the layout file, but when I download that, it's the original one used on the site. I really don't know much about computers but would like to move the menus around and can't do it. Please let me know if there's something I'm doing wrong. Thanks!

It does. When you have the Advanced Layout Options enabled, and you move menus around, add new menus, whatever, the layout file you've uploading using the Advanced Layout Options does not reflect those changes.

So you'll need to go in to the layout file, and modify it accordingly, or you can regenerate the file, OR you can disable the Advanced Layout Options.

The problem that I'm having is when I generate the layout file, it's not the one that I adjusted, so when I test it, it reverts the site back to the original. The same thing with the menu file. It took me forever to figure out how to get rid of the boxes around the different menus and I would hate to have to start all over for that. Any help would be great, thanks so much.

Hopefully I'm not doing something stupid, in which case, sorry!!

Just look at the layout file that you had used to deploy your site for the sections that look like <!--System:Menu:XXX--> And modify/add them accordingly.

I figured it out finally, thanks so much.

Awesome.