So right now I have made it to Novac through Nipton and i haven't made any main quest progress there. I have ED-E, actually he's at Nipton because he love ruining all the fun I have blowing giant ant heads off with my silenced varmint rifle. I have not taken him to the scrap yard, i was planing on it because i assumed there would be some trade of for rex (paying homage to dogmeat from FO3). Did I already secure ED-E as my non-human companion for the game?

Also, in Nipton I talked to then killed Boxcars and failed the quest, (I thought he didn't care!) I fought a bunch of Legion troops with some NCRs which i came to find out is esentially the quest with out the 100xp reward. For the wheel of fortune quest that i will not be able to get, can i still get all the items i just have to go about it on my own accord?

You can fire ED-E and get Rex... then you can fire Rex later and pick ED-E back up.

I killed him also, failed a quest, but gained karma for it. Since I wasn't sure what the quest was for, I just loaded the auto-save from entering the building and left him alive. Have yet to find out what the quest is or where to get it from though.

Ok cool! So even if I bring ED-E to the crap yard and continue his quest I can always fire him? How do I fire companions anyway? Fallout wikia basically says that the quest boxcars gives you is usless, you get 100xp and maybe adds to some quest completing achievement? I unknowingly did all the quest asks for, almost died killing legion guys too.

Choose the option to talk to your companions and you'll have an option to fire them. (Usually the second to the last item on the list I believe.) They'll then go back to where you found them or somewhere in the Strip. (I've heard people say they'll go to the Lucky 38 in the Strip, but when I fired Boone, he went back to Novac.)