Forums / Cotonti / Support / Site navigation row in header.tpl

You don't need to read anything from the URL. Use sed_import() and import those from GET parameters as normally. Even if your link is:
mysite.net/cat1/subcat1/alias.html
you can still get alias as normal:
(note: for page.php it will already have been imported even if you hook into header)

And so is for mysite.net/cat1/subcat1/.

URL transformation was designed to be as transparent as possible, so that all the rest works like if there was no transformation at all.