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Medications for RA usually take a while to build up in your system and that means that the longer you take them, the more effective they become.  If your son is cutting down on Naproxen because he feels he doesn't need it as much anymore, that's a good thing and a sign that the Methotrexate is starting to work.  However, even though the disease modifying drug (like Methotrexate, TNF blockers, etc.) is working, you can usually expect to still need painkillers, just not as many as without the medication.    Medications for RA also have a tendency to be really hard on the stomach.  I recommend that your son talk to his rheumatologist about his problems - it's a common side effect and I'm sure the doctor has a number of suggestions.  Over-the-counter medications such as antacids can help, as can eating bland food the day after taking the medication.  Peppermint tea, hot water with a small slice of lemon and ginger tea help settle the stomach.  He can also try taking acidophilus every day (or eat one of the probiotic yogurts) - it helps protect your G.I. system.  Depending on your son's specific stomach issues, there's also prescription medications such as Losec or Pantoloc that may be helpful.  All of these suggestions may help your son decrease the level of nausea to a point where he can live with it, but if it becomes intolerable, he should certainly speak to his doctor about alternatives.