To start with a default mapcycle for a particular game mode, simply choose the mode you want and then delete everything in the mapcycle entry box. When you submit the form, the "Easy setup" page will fill it in for you with the default playlist for that game mode.
For the new mode to take effect, you'll need to wait for the next map change (if you'd like to speed that up, you can trigger a map change manually with the "admin.runNextLevel" command through rcon).
You can also use our NFO map cycler to mix game modes. To have the system fill in a default cycle for you, just check the map cycler box and then submit an empty list; it'll put in alternating rush and conquest maps.