You don't need a separate chart note, I often see an additional paragraph at the beginning that addresses the problem(s), something to the effect of: "Of concern today, the patient does complain of intermittent left knee pain with swelling after doing yardwork this weekend." That is sufficient for the history. As you addressed earlier, the exam can't really be counted since a complete physical is already being done. Since you only need 2 of 3 key components, the final factor is the medical decision making complexity. So in the assessment and plan it should indicate if over-the-counter drugs or prescription drugs are given, if any tests are done, referrals to see a specialist, etc. That will help you determine the medical decision making complexity for the 'problem-oriented' portion of the visit. That's not part of a normal preventive exam.
Of course any minor or incidental findings are included in the payment for the preventive exam. Only something requires extra work (even if it is just significant cognitive labor) should be billed separately. Make sure that is clearly documented.