Adding your plugins into plugins.js
is just a recommendation. You can add you script tag to your page if you are more comfortable with that, it's up to you.
But to answer your question, the idea of the plugins.js file is to keep all your plugins in one file so it's just a single request for all your plugins instead of multiple request for a bunch of different plugins.
the best way to do this is to minify all your plugins and copy and paste that minified code into your plugins.js
file separating them with relevent comments. Like so:
/*
* jQuery Form Plugin; v20140218
* http://jquery.malsup.com/form/
* Copyright (c) 2014 M. Alsup; Dual licensed: MIT/GPL
* https://github.com/malsup/form#copyright-and-license
*/
;!function(a){"use strict";"function"==typeof define& ...
/*
* Another plugin
* plugin info
*/
;!function(a){"use strict";"function"==typeof define& ...
You can use an online tool like jscompress to minify your javascript files for you.