It shouldn't mess with your updates as long as you add them in their own php code chunks... so it would look like:
<?php
//your custom code
?>
<?php
// code produced by the Server behavior
?>
<?php
// more custom code
as long as you add them to their own code section they shouldn't be messed with.
(btw I noticed you have some blank lines in your code between ?> and <?php on the top of the page... that can cause issues in php and the blank lines should be removed)
?>