Menu Writer and Nested Templates

I am attempting to create a site with a set of buttons in a left vertical nav panel. This set of buttons will be identical on all pages in the site. I have created this and saved it as template1. I also want to have a set of horizontal nav buttons across the top of my pages for each main "section" of my site.

I want to open template1, add the horizontal nav buttons in the appropriate div at the top of the page and save this page as template2. I will then open template2 and create all of my content pages for this particular section. I will repeat this process for each section - creating a new template with the new horizontal nav buttons.

I can easily create template1. I have been attempting to create template2 but am having difficulty. In template1 I have made a div called "topnav" which is right under the header and made it an editable region. I then create a new "page from template" using template1. After this page opens I use menu writer and insert the horizontal menu in the editable region. When I try to save this as a template I get a message saying:

"You have made changes to code that is not marked as editable. If you retain those changes they will be lost the next time you apply a template update to this file. Do you want to retain the changes until then?"

If I try to ignore this and move on, it doesn't work. If I create pages from template2 and save them, all is well. But if I try to make changes to template2, the pages derived from template2 do not update. Curiously, changes made to template1 DO take.

Why is this happening? I have inserted the menu into the editable region. Why is it saying I am making changes to code that is not editable?

Is there a better way to create nested templates and still be able to use menu writer?

Any help would be appreciated.