"How do you set up variables in the URL? "
http://www.mysite.com/page.php?category=general
then you would do something like
$category = $_GET['category'];
to get the value
"What does Include do: does it run a seperate php script at that point or what?"
yes basically, it adds the code in from the file where u call it
"And If the included php is a search engine, can I still use that search engine on that moment?"
yes should be
Sorry im not sure about your last question ill look it up tho