Like Jim said, don't let the math fool you. Yes, 6 eigths notes equal the same amount of time as 3 quarter notes, but it's more of a feel issue.
As I mentioned, "El Paso" feels more like a "two feel". In other words, try singing the first line to yourself.
Down in the west Texas town of El Paso
The accents fall on "down", "west", "town" and "Pa".
Down in the west Texas town of El Paso
"Down in the west Texas" is all one phrase, with two accents... thus a "two" feel, thus two sets of three, thus 6/8.
At least that's how I hear it.