So I finished up the quest "You gotta shoot em in the head" and gave all the keys to that Crowley character. I was wandering around the wastes today and I came across Ft. Constantine. I wiki'd it and found out you need the keys that you give Crowley. I went back to underworld to try and find him and kill him to get the keys but he was nowhere to be found. Am I screwed or is there anywhere I can find him and get the keys back?

You should be able to get into the fort by yourself just fine. Those keys unlock certain access doors within. You need those keys to explore the entire area. Try looking around. You might find a dead Crowley in there. I have either:
1. Killed him, or let a companion kill him in Underworld.
2. Followed him on his long and amazingly, torturous route to the fort, then killing him at the front door.
3. Done as you did, then traveled to the fort and found his dead body, with all the keys.