Do I have a better chance for a PhD in a field I have research experience in or one I have had better courses on?
Apply for and do the PhD you actually want to do. 

The skills gained by having research experience are generally subject transferable, so if you want to do theoretical computer science, explain what skills and knowledge your research experience in computational biology gave you that would be applicable to that field. It could even be something as simple as saying "my experience in researching x topic in computational biology got me interested in computer science as a field of research, which I want to explore further, focusing on theoretical topic y".

Don't try and game the system. Be honest about your interests and the experiences that have led you to them.