Eating while on protocols is covered in the book. Here is some of that info:
Do not take an MMS1 dose with your meals, space out food consumption and your MMS dose by 20-30 minutes.
During the hours you are actually taking your MMS1 doses, try not to eat big “feast” types of meals, but rather eat smaller meals and/or snacks.
Do not eat or drink things that neutralize MMS1 during your dosing hours. (see pages 35-40)
Regarding taking Naproxen 550, if you need to take it during dosing hours, then do that. Otherwise, take it one hour after the last dose of the day. There is probably no interaction between Naproxen 550 and MMS, so you could take it when needed.