How do you handle having side projects with your employment contracts?

I'm about to deploy a data mining web app and I've got an interview data engineer. The side project and job will have many crossovers in terms of work and I'm wondering about the implications of IP assignment and conflict of interest. I've mentioned my app in earlier discussions with the company and it stands to reason that it probably helped me get this interview. I'm curious if others have been in the same situation and/or know how I should go about protecting my IP?