If I can give an analogy to understand it better, you can write a program in the old fashioned way where there is just one class and hundreds of variables and functions in that - which does the job for you but is a nightmare in terms of maintenance, and you can write the same program using Object oriented methodologies. There are no tools to convert the old program to use OOPS methodologies - it is about learning OOPS and then refactoring and improving your code.
Probably I can give you a reference of some best practices of how not
Refer this link for some jQuery examples and best practices
JQuery Examples and Best practices
In-case you are totally new to the whole jQuery, please see SA's solution #3 for some references about it.