For many projects, this question will have an obvious answer. A study of the airflow around different wings belongs in Aerodynamics, whereas a study of developmental biology of fish belongs in Zoology. The question of category choice arises only when there are several aspects to your project, and those aspects in isolation would seem to suggest different category choices.
There is a single simple rule for choosing your category: Your category should match the focus of your study, and is independent of any tools you may have used during that study. As an obvious example, if you wanted to learn about human behavior but you had to use statistical tools to deduce your conclusions, that project belongs in Behavioral Sciences and not Mathematical Sciences because the math involved was simply a tool, not the focus of your study.
An alternative way to decide this question is to consider the kinds of questions judges will ask that you are most interested in answering. For example, if you constructed an electronic device to enable you to study some astronomical phenomenon, you should ask yourself whether you want the judges to talk with you about your electronic device and how clever your solutions were while constructing it, or whether you want them to talk about the astronomical phenomenon.
Those two considerations are simply different aspects of the same question. What was most important to you was probably what you focused on, even if you may have spent more time dealing with peripheral issues. That subject focus determines your category.
The world is full of interdisciplinary projects. Somebody will write a play that discusses quantum physics, or someone will develop a new method in artificial intelligence to diagnose cancer. The California Science and Engineering Fair (CSEF) has seen an explosion of projects in recent years that apply AI and machine learning tools throughout all subject categories. However, each project at CSEF is placed in one and only one subject category. CSEF does not create explicitly interdisciplinary categories such as Artificial Intelligence Applications in Biochemistry. Therefore, you will have to choose one and only one subject category in which to place your project.
Your selection has consequences.
CSEF judges include world experts in their fields. Their expertise may be in space science, mathematics, microbiology, and so on, but nobody is an expert on everything. That includes our judges. If you enter your project in the Biochemistry category, you are going to meet with biochemists and molecular biologists. You can be sure that the judges will understand the biochemistry and molecular biology involved in your project, and that they will judge you fairly. However, you cannot assume that these judges are also experts in artificial intelligence, so you should therefore not expect that they will credit you for any original work you may have done in artificial intelligence.
This applies generally to all categories. CSEF judges are expected to be experts in their field, so they are required to evaluate your work in the subject category you chose for your project. However, since they are cannot be experts in all other subjects, CSEF judges cannot be expected to fairly evaluate work you may have done outside of your chosen category. Consequently, CSEF judges are not required to evaluate any aspect of your project which lies outside of your chosen category. Further, since non-expert evaluations are generally unreliable, CSEF judges are not required even to give credit for any work you have done outside of your chosen subject category.
This is the most serious consequence of choosing your category if you have a truly multidisciplinary project. The category you choose determines which aspects of your project will be evaluated by your judges, and which aspects they can ignore. Think very carefully about this consequence before choosing your category.