You mean "emulsion or emulsifier" tubes? Shouldn't matter other than they shouldn't be put in upside down, and not sure even if that's possible. What bike? I think the 500/550s only go in one way. Not sure how you could accomplish aligning the holes.
The 750 early style carbs are threaded in. Don't over tighten them, or the tube will butt against the needle jet and bend. Snug them and leave em' alone. its normal for there to be some threads showing after you've snugged them. And be sure the main jet on a 750 is snugged up into the bottom of the tube. If they are loose, they fall out into the bowl, and you suddenly have a driveability issue that'll leave you scratching your head wondering.