Since your only two are options are to side with the NCR or the Legion, does siding with the NCR have some kind of affect if I'm going for an independent vegas playthrough? NOTE: I'm on good terms with the NCR, Legion hates my fine ass, and during my battle at Hoover Dam before I started this quest, I fought along the NCR to the end. Hope that helps, and thanks for any help.

Nope. First time through I had them side with the Legion so I'd have a halfway decent fight at the end of the game. Most people have them go NCR though.

Have the remnants side with NCR if you want to have them as allies, Legion if you for some absurd and childishly primitive reason want to murder them in cold blood, those fine men of the United States Army.

LOL I sense no bias in this post

Here, drink this water.

No, the burning sensation in your lungs is not because of the water.

DRINK FASTER.

Having them side with the NCR will have an effect - for purposes of the game, they will be allied with the NCR faction. So if you piss off the NCR faction (ie you get caught installing Yesman's chip into the Dam control computer), the remnants will be hostile to you since being caught will turn the NCR hostile to you.

To avoid this, either sneak by the guards, or use speech to convince them that Colonel Moore needs help.