Is it a bad idea to interview for the same job in two different locations, for the same company? Am I breaking a moral code here? Don't want to ruin a shot at either job.
In some companies with a lot of locations they actually ask during the application process if there are other locations that you are willing to work. They do this so that you are in the pool of applicants not just for one store, but also the one a few miles away.
In companies with franchises it is a little more complicated because they are separate companies. One owner may have one location, but the restaurant just down the road could be owned by somebody who has a dozen.
Applying to more than one position/location is not a problem. Though if they are ready to offer you a position they will ask you to withdraw your other applications with the company.
I can't see anything wrong with it, you're applying for two separate positions which doubles your chances of landing a job. It all looks above board unless there is something you're not telling us.