There is absolutely nothing wrong with submitting a bid for the second position. If the recruiter asks about it, you simply tell them that you really want to work for Southwest and are interested in both positions. If you are offered the CSA position, you can choose to accept it and withdraw from consideration for the corporate position. Or you can pass on the CSA position if the corporate position is a better fit for you.
Personally, I would accept any position you're offered at Southwest so that you can get your foot in the door. Once you're in, your opportunities are unlimited. I encourage anybody who wants an airline career to start in a front-line job such as CSA first and then move on to a corporate job. Having first-hand experience with the Customers and the daily operation gives you a certain wisdom that serves you well throughout your airline career.