How can I call a PHP Function inside a Javascript Function? This is what I have so far, but I don't think I'm doing it the right way.
Any suggestions?

PHP Code:

<?php
function phpQuery(){

     $query = mysql_query("INSERT INTO mytable VALUES('','name','email')");

}
?>
<script type="text/javascript">
function delayQueries()
{
  timeoutID = window.setTimeout(doQueries, 2000);
}

function doQueries()
{
  var runQuery = "<?php phpQuery(); ?>";    
}
</script>

I dont think that will work.

However you could use ajax to call a separate .php file with the php sql query in it. ?

The javascript function will be executed by the clients browser, it seems you are lost in the "Server / client" relationship snafu. To execute a php function on the server you will have to send a request (probably ajax) for the page to the server, the php on the server will then need to return the results to the client browser. If you need some help message me and we can confer in a chat.