You can't expect ER docs to know how to treat AI diseases like lupus. They are just for times when you can't see your rheumy. Time to go to your rheumy or even get a second opinion. If plaquinel is not controlling lupus then another treatment should be considered. Plaq is just a first level of treatment and there are much more powerful meds or combinations that could be used. Of course, no one wants to be on pred any longer than needed. I have been taking pred since mid 2005 but the dose is so low now there are no side effects and probably no theraputic value....who knows.
I see many who go on and off meds and have a perpetual roller coaster of flares and temporary remissions. Not good. It takes a long, long time to get an immune system under control and some patients need controlling meds indefinitely.
Your headaches could be lupus related or something else. You need to be alert if they continue and find out what it is.
As for communicating I used to prepare all my questions in Word and ask them one by one. The first time I visited my rheumy at Northwestern I had 26 questions.....he and his associate answered every one of them patiently. Now I have few and the main debate I have is getting off my meds but that is another subject.