W3TC does not have any option of its administration GUI to manage or change the priority for the insertion of minified CSS and JS through WordPress. However, it does provide several macro comment tags that will force the minified JS and/or CSS files to appear at the position where the tags are placed.
These W3TC’s macro comment tags are as follow:
<!-- W3TC-include-js-head -->
<!-- W3TC-include-js-body-start -->
<!-- W3TC-include-js-body-end -->
<!-- W3TC-include-css -->
How you use these W3TC HTML comment tags to embed the combined JS and/or CSS files at the location and priority you prefer? Edit your active theme’s template (e.g. header.php, footer.php, single.php and whatever other PHP file that constructs the part of HTML where you want the JS and/or CSS to appear), and insert the the appropriate tag above at the location or position, then save the file.
Which tag should you use? In both auto or manual minify mode, W3TC will place the minified JS files in the following three embed location:
Embed in <head>
Embed after <body>
Embed before </body>
The priority or the actual position of the above JS embed location by placing their corresponding comment tags at your preferred location.
<!– W3TC-include-js-head –> (Embed in <head>)
<!– W3TC-include-js-body-start –> (Embed after <body>)
<!– W3TC-include-js-body-end –> (Embed before </body>)
The minified CSS is always embedded in HTML header near the beginning. To change the position, place the following comment tag at your preferred position.
<!– W3TC-include-css –>