I doubt it hurts to get rid of them.
One alternative, though, is that you can set up vhost entries in your Apache set-up that will allow you to create local domains that each point to whatever directory you want to use. That way you could, say, have "myproject" point to some directory on your computer where you want that project to reside. With a vhost set up in your apache config (and after restarting apache), plus a hosts file to tell windows to send requests to "myproject" to your local host domain. If that interests you but it's all Greek to you at the moment, we can probably walk you through it (or find a good video).
