Jquery loaded at the bottom of the page

Jquery loaded at the bottom of the page

I'm having problems with something that is probably pretty basic, yet I can't quite figure out what to do.  Lots of sites link jquery in at the bottom of the HTML document.  This seems to be the recommended practice.  What I don't understand is how to use jquery earlier in the page when that happens.  I try to put a simple script on a page, which I've test and know works, but if the Jquery is loaded last, it doesn't work. 

I've read up on using  $( document ).ready() and the short hand, but that never seems to work.  I'm doing nothing complicated, just changing CSS or doing html edits.

So what am I doing wrong.  My scripts work perfectly if JQuery is loaded in the header but they don't work when it's loaded near the end of the html file.