Separate Search Service Application needed for a separate file share?

I need to have a search screen that will search the contents of one file share only. I want this to be totally separate from the main search. I created a new Search Service Application, crawled my file share, and then created a new site collection for it. I then go to Central Administration -> Manage Web Applications, and "Service Connections". From there, I change the "Edit the following group of connections" to "custom". I can then pick my new Search Service Application, and set it as the default search application. That makes the file share search work, but the main search breaks. What is the proper way to maintain separate searches? Am I going about this wrong?