Different templates for index, archive and comment

I’m sure I’m missing something really obvious, but I’ve got a site with twin menus on the front… so, when rendering inline comments it gets mighty cramped (especially given that I’m using the threaded comments plugin). Switching to pop-up comments is a possible workaround, but not a complete one — the permalinks still run the comments inline anyway, so same problem. The answer is obviously to have seperate templates or stylesheets for the comments and archive pages… but those are automatically generated from the index layout, can’t get rid of the menus.
So where’s the right spot to code something like that in?
-p