1 - Avoid the use of IDs for generics, always use classes instead.
2 - Prefix the classes on HTML generated by plugins you are creating with some name space. i.e.: js-plugin-foobar-nameOfClass
You can avoid having the user add a ".js" and a ".css" file for each pluggin. You can generate css classes with javascript. That way you will only have to import one file for each pluggin: How to dynamically create CSS class in JavaScript and apply?
Take a look at the jQuery widget factory, you can build your plugins to use it, and that should facilitate your life. They also have some coding guidelines: http://jqueryui.com/widget/