As a solution to my original problem with adding an option to edit custom files within admin pages, I decided to simply let users upload their own files, and edit the through the WordPress Theme Editor. The problem is, the user can find those files if they know the naming scheme, but they're still hard to find. Also, if I store a file under known names such as "header.php" (in a sub-folder, but still), they show up like template files from the default template heriarchy (which is rather confusing).
Is there any way to manually add the files with custom names to the Theme Editor? I know custom template show up as "Template X" when a name is defined in a comment like so:
/* * Template Name: Something-or-another */
but these aren't technically page templates, so I'd rather avoid such hack.