I am looking to buy a bosal system for the 02 protege sedan. So do I want a cat back system or one that replaces the cat???? Does this replace the primary, secondary or both? What the hell is the difference???

 

There is a federal version and California version. Federal version has a resonator but no cat convertor. Cali verson has a convertor but no resonator(does the Cali version come with a convertor or just a space to keep the OEM one?) In both cases I am referring to the secondary cat. The primary is located just after the exhaust manifold.
Do some searching on this engines search page. You will find posts where people post their bosal setups. I think MP3-Owner has some nice shots of a car hoisted up so you can see the piping very well. His is a federal version.

 

Thanks for the explanation I have placed the order!