You can use str_replace in your php code:
http://php.net/manual/en/function.str-replace.php
$search_qry = "Whatever%They%Type";
$replace = str_replace($search_qry, "%", "-");
EDIT:
In the case of your strings - they have spaces, which show up as % in a URL, so use this before you do your $_GET
$search_qry = "Whatever They Type";
$replace = str_replace($search_qry, " ", "-");
EDIT 2
Since this is a $_GET - Javascript will have to be used to clean the string before it's sent. (using jQuery and javascript here)
<script type = "text/javascript">
$(document).ready(function(){
$('.example-input').blur(function(){
var str = $(this).val();
var clean_str = str.replace(" ", "-");
$(this).val(clean_str);
});
});
</script>
This should clean the string in the input box before it's even sent through the get.
or instead of .blur, you can use $('submit-button').click(function(){...
Or, you can use the .htaccess file to do a mod rewrite. But I don't know that well enough.