All those links were automatically added from the auto discover process. You might want to turn off auto discover.
With that view you really have no idea where traffic is going. Right click on the map, select add link, place the link between two devices you know are connected to each other. Select the device, mastering type "snmp", change type to match the link speed. Find the interface in the list that is connected to the other device in the interface drop down list.
I put a speed on there so it changes color when there is some traffic. You might delete the other lines if they are not helping you map your network. Also back up your DUDE folder before and after you have made big changes.
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