I get the sense that you believe jQuery and its UI is mostly CSS. I would say its mostly functions and objects. Most (if not all) jQuery objects can be accessed so it is possible to use CSS to change their appearance, or trigger CSS actions. I don't see your issue, at least as described above.
You might try throwing something together quickly on jsfiddle, as a test, and try to do whatever is bothering you. If/when you hit a wall, post some code here, and you'll probably get some help.