There might be, but what I know of SmartNavigation is though my own
questions on newsgroups. I have not seen any article that documents the
architecture's behavior.
It may just come through trial and error as you determine what does and does
not work.
Basically, here is how SmartNavigation works. When you turn SmartNavigation
on, the page is rendered with a hidden iframe (visible if you view the
page's source). This iframe is the container for all submit requests. If
you click the submit button, the form data is copied to the iframe and
submitted there. The iframe then returns from the server and some
JavaScript will copy the DOM from the iframe to the main page. That is how
the browser can stay at the same place, it is never reloaded.
If you dynamically create JavaScript that is returned from the server based
on posted conditions, then you may run into problems because the JavaScript
will run in the iframe, not the main page. Also, you cannot turn
SmartNavigation off once it is on because the main page is never refreshed.