I ended up using a <base>
tag in the header, and then wherever I needed anchor links I used php like so: <a href="http://<?php echo $_SERVER[HTTP_HOST] . $_SERVER[REQUEST_URI];?>#">
This makes the link go to the current page with a # added to the end, so it's the same as using <a href="#">
Let me know if you think I could have done this a better way! Thanks!