Arrays used here will be treated as values pertraining to a single entity. For example, if you use %name()|%age() it should mean that you have a list of people and that those 2 arrays represent the names and ages for each person, where %name1 is related to %age1, %name2 is related to %age2, etc.
This means that when you perform any action on them, all of them will keep their relations intact.
For example, if you have the %names() array with the values John,Anne and the %ages() array with 23,17 that means that John is 23 and Anne is 17. If you sort these by name, the resulting arrays will be Anne,John and 17,23. As you can see the first name is still related to the first age, and the second name is still related to the second age.
You can input multiple arrays either by hand like for example 1,2,3|a,b,c or by using Tasker variables like for example %numbers()|%letters(). Both will function equally.
You can change the separator of individual array items (, in the example) in the Item Separator field. You can change the separator for arrays (| in the example) in the Input Arrays Separator field.
This is easier to explain with an example:
If this option is NOT selected, your input can be something like the %names() array with the values John,Anne and the %ages() array with 23,17.
If this option IS selected, your input can be something like the %john() array with the values John,23 and the %anne() array with Anne,17.
This is useful to read CSV files for example in which each line of the file will have the vertical format.