One option is to be rigourous about separating your application logic from the view related stuff. What this means is writing a layer between the mod_perl data structures and your internal objects, then you write a thin layer which converts from an Apache::Request to your internal Request structure and pass that inwards. The application should then return a datastructure/object/lump of XML that you render to HTML using the templating system of your choice.

That way you get to test your application by feeding in appropriate internal Request structures and comparing the returned data structure with what you expect (and, of course, you should also write tests to ensure that Apache::Requests get converted correctly and that your data structures are rendered properl, but these sections can be tested independently of the application itself and can probably (in large part) be tested without needing to run Apache. Only when you've got your automated tests passing will you need to restart Apache (or use Apache::Reload) and do the eyeball test.

You do have automated tests don't you?