boballoo,
You really have not given information about what sort of problems your users are actually having.
I am going to guess that some users are disabling cookie support (or some firewalls are blocking cookies) which results in your web apps failing.
Many apps generate a "session id" to identify a particular session. These session id's are typically stored in a cookie and thus, disabling the cookie will disable the application. For many apps, this session id is the only thing being stored on the client and thus is the only thing we need to be concerned about.
If the original developer used standard php session functions then there is indeed a .htaccess setting which allows storing the id in the url. Tweaking this setting may in fact be all that's needed so I would suggest trying it first.
However, it's possible that the developer did not use standard php session handling. It's also possible that the developer may be using cookies to store information besides the session id. It's also possible to write code that use's the standard session handlers but still will not work after adjusting the cookie controll settings.
Having some idea of how cookies and sessions work is esseintal for making these kinds of decisions. Here is a starting point:
http://www.php.net/manual/en/ref.session.php