The USNA only cares about the Math/English sections. Your nomination sources may want to see the writing score (Writing was at one point optional). If you have a Writing score - fill it in. If you do not, make that known.
Don't be concerned about contacting your nomination source's POC for clarification. They are there to assist you and anyone that has worked in a Congressman or Senator's office is quite familiar with helping people complete bureaucratic forms. If you do call, suggest you thoroughly review their requirements in advance so you can get all your questions answered in one session.