When I am coding a template, specially if I want to make it for someone else I usually add notes, because I want people who are not that experienced with coding to understand what they have to do. So the way to add comments in different files it:
For .CSS files
For .PHP or .HTML files
Inside PHP Codes
<? php; /* This is how you insert multiple
lines comments */
And this is all. Now if you ever want to leave comments in your coding, this is the way you do it.