What would be the best way to call two arrays (identical structure, just different values)?

Your question is not very clear, but sure, you can define as many arrays as you want in the doc-level.

If the arrays have the same structure and length then you can iterate one of them and use the index of the item you're interested in for the other. For example:

var array1 = ["A", "B", "C", "D"];

var array2 = [65, 66, 67, 68];

for (var i=0; i<array1.length; i++) {

     if (array1=="B") app.alert("The number matching B is: " + array2);

}