You can create a "recipe" through your client, generating a .dsr file: http://sledgehammergames.com/blog/view/98
. Then, upload this to the server, either by using the FTP or by creating a new .dsr file through the "File manager" page. Finally, set your map rotation (default.dspl) to use that .dsr file for one or more of the maps.
Instead of creating a new .dsr from scratch, you can also edit an existing one on the server. The easiest way to do this is through the "File manager" page in the control panel.