I think that what may help you is AJAX. AJAX is when JavaScript communicates with the server-side programming, the PHP. One good thing about AJAX is that the web page doesn't have to be refreshed, an update of just part of the data can occur without refreshing the whole page.
JavaScript can access what's called the document object model (or DOM). The DOM includes all of the HTML elements and all of the CSS styles on a page.
JavaScript can, between accessing data on the server with AJAX, and accessing the DOM to get or change the web page, do a lot.
One thing to watch out for is that JavaScript can be turned off in a web browser, but you can just be aware of that and have your web pages that rely upon JavaScript have an error message that's displayed when JavaScript is turned off.
AJAX, since it accesses the server, has security concerns too. You'll need some sort of login (which you have anyway for eCommerce) but I saw a whole book that talked about AJAX and security.
AJAX Tutorial:
http://www.tizag.com/ajaxTutorial/
JavaScript DOM Tutorial:
http://www.w3schools.com/htmldom/
You asked about jQuery. You may know this but jQuery is written entirely in JavaScript, it does things for you that are commonly needed in JavaScript. The advantage of jQuery is that the code is already written for you, the drawback is that there's that much more to learn. jQuery's especially useful when you want to support multiple browsers.