It looks like you’ve overlooked the 5th input parameter of:
wp_enqueue_script( $handle, $src, $deps, $ver, $in_footer );
Namely the boolean $in_footer part, that will put the script in the footer, if set as true, else in the header.
You can also use $deps to handle dependencies.
Check out the Codex for more info.
=> I would stick to wp_enqueue_script() and not manually place the scripts into the header or footer.
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