Linking and Combining JS and CSS files

I have a custom master page where I am currently linking to a javascript file the traditional way seen below.  What I would like to do is include my javascript in the master page, but have it combined with any other js files.  My CSS file that is in the theme folder is automatically being called by my site but it is not combined with any other css files either.  My question is, how to I properly call CSS and JS files in either the master page or on a given page and make the 'Combine script resources' and 'Combine style sheet resources' features work. I have both of them currently set to True under Advanced Settings -> Page Settings.  I'm currently running Sitefinity 5.2.  Please let me know if I can provide any other information.