I lost Ed-E in one of the vaults and he never followed me out. I've since hooked up with Victoria but other characters can still see ED-E even though he is not actually there. Do I need to check all of the vaults for him so that I can tell him that we need to part our ways or is there an easier way for me to send him back so that I can continue on in some of the other quests?

*Veronica.

You can dismiss ED-E by using on of the Companion Dismissal Terminals located on the Gun Runner's Hut (Store) or inside the Lucky38 before you go up the elevator.
Using these should dismiss ED-E back to the Nash's House in Primm

I lost him at the Boomer's base by the solar panels and the same thing happened to me. I forgot about him after a while, got a DLC for the game, and then when I came back he was back at Primm...

*Lonesome Road DLC no doubt fixed it when you acquire the ED-E Clone there.