Please Note: The following screencast was created using Dynamik Website Builder, but is completely relevant to Genesis Extender since it shares this same feature.
What Does "Enqueue" Mean?
Using the wp_enqueue_script function is the proper way to add javascrip files to your site.
Choosing Where To Enqueue Your JS File
If you've enabled the "Place In <head>" option then your JS file will be enqueued into your wp_head() hook location, placing in the <head> of your site. By default your JS file will be placed just above your closing </body> tag.