Huh? In my case I just started the website and I see the DKP menu at the left, but no other menu items. Then I got to menu admin and I see there are a number of menu items in the DKP menu. But since several in the guild now have DPK I don't know why it doesn't show. One thought was that there was some kind of way to identify which DKP system is displayed there. I only have one (default) DKP system right now .....
Most of the items in the Admin Menu are just for managing the DKP System you have setup. There typically is only 1 menu on the Main page for DKP and typically has 4 links in it for showing things like Current Standings and such.
If you have more systems more menus will appear provide you are not using an Advanced Layout with a custom layout.html file. If you go the Advanced route you will need to insert the correct tags into the page for each system.