Well, I played with ContentFilters and set it to "0" to turn all filters off. That let me write script and keep it in the editor. 

What it still won't let me do is to edit the html and put unbalanced tags into the content. So for a template editor that I use I can't put <table> in the header box, <tr>...</tr> in the iterator section and </table> in the footer section. Worse yet, if you forget an opening tag for any piece of content while in HTML mode, you just loose all of the markup for the section. So don't forget that <table> or you will loose ALL of the <tr> and <td> tags.

I fear I will have to go back to Fck until we can figure out how to work around this. If I just go to "Basic Text Box" and edit it, then change back to HTML editor somewhere else, then visit my editing page it will blow up the layout.

 Chris, what module is requiring you to put layout in the RTE?

Doesn’t Mushroom use .htm files for templates which you could ftp to update?   From their site: “Template editing can be done in 2 ways either using a plain text editor because most experienced users prefer or a GUI editor.”  Sounds like you should be able to configure this. In any case, I would contact them about using plain text fields for your application.

RTE is best reserved for discrete blocks of content the end user will manage.