I usually picked 3. For most schools, this part doesn't matter. It will matter for the specific secondaries. Either they will have similar checkmark boxes with areas tailored to their programs offered or they'll have space (with very, very limited character counts) to say keywords that align with your research interests. They then use this information to pair you with faculty if they can't match you with ones you requested for interview. In addition to research interests, most will have departmental selections to which you're applying - sometimes for official purposes so they know you're explicitely applying to the school of engineering for your PhD.