Load jQuery in wordpress footer section will be best
I you want the minimize functionality for your in page pop-up use following code for minimize and restore button. Following code you can use for showing the minimize button on pop-up.
Note: Here for this example My in page popup div id name is “popup-container”. For using following example you should keep the main popup continer id name is “popup-container”.
<a id="dialog-minimize" href="#" onclick="minimize();" style="display: block;"><span>Min</span></a> <a id="dialog-minimize-return" href="#" onclick="minimize_restore();" style="display:none;"><span>Min</span></a>
wordpress and jquery conflicts – How to solve that
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jquery tips for wordpress theme developers