[eluser]BrianDHall[/eluser]
Other than how CI handles url segments and by default does not use GET queries, jQuery works with CI just like it works with anything else in PHP, no difference.
You can easily go to the jQuery site and learn jQuery and should be able to apply what you know to CI with little or no adjustments.
Same thing with learning CI. CI and jQuery together isn't much different than using them alone.