Don’t get hung up on understanding things to try placing them in your designs, and flying by the seat of your pants. Some of the jQuery coders are straight up rocket scientists creating the code that is plug n’play.
Whilst yes there are loads of plugins available for jQuery (and other Javascript libraries) which are pretty much just drop in and they work it is still nice to understand what is going on under the hood so to speak because if something changes on your server which stops something from working and you have no idea how it works in the first place then you could have a pretty big fight on your hands getting it all back up and running again.
The way I feel is best to look at this is to create your site without any add-ons such as Javascript and ensure that you have a fully working compliant site without such technologies so that anyone visiting your site with these disabled can still get a good experience. After that you can then add in all the flashy Javascript and Flash technology for those that have them enabled.
This way you cater for everyone’s needs at no expense to one or the other. Then once your site is up and running and everyone is happy you can go back and look into how the plugins actually work so that you can have a really good understanding of what they are doing. Sometimes just understanding how something does work can give you ideas to getting the same effect or end result without using assisted technologies in the first place.
Just my two penneth worth though 😉
Best wishes,
Mark