If you set any compare function to Compare Aggregates (by right-clicking on it), the comparison works through both arrays comparing the elements that are at the same index. The compare output is True only if all individual comparisons were True. For example, if you're comparing aggragates on two arrays, a[] < b[] is True if a[0] < b[0] and a[1] < b[1] and ... a[n] < b[n]. You can also compare aggregates on clusters if the structure (including cluster order) is the same.
In case you wanted to compare individual elements, you can right click on the comparison function and choose to compare aggragates or elements (returning an array).