All JS that is properly enqueued will be added to your header at the very point where you, or the theme designer, respectively, included wp_head()
.
Ideally, you should also enqueue your custom script(s) the same way and make them dependent on jQuery – WP will then naturally load them after.
If however you want to (as I assume your are doing now) include JS manually in the header, then do so simply after wp_head()
, if the JS depends on jQuery.
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