I was on 4 planes in the last 2 weeks, and I have to say that things have really calmed down and gotten easier to handle at the airports. The quart-size clear sealing bag is only for liquid or aerosols like shampoos, toothpaste, hand lotion, etc. Medical liquids that are in their original containers (like TOBI or saline, insulin) are exempt. Also, the carryon limit does not apply to a bag containing medical equipment (but still, try to be reasonable about what to check and what to carry on.)
As for it being embarrassing, don't worry about it. Everyone is so busy trying to take care of their own stuff that it won't be an issue. Even the TSA agents won't look at you weird. I actually got a little sympathy on the last trip...the guy looked at all my stuff and said "Wow, I'm sorry."
This last trip I had all my meds and my nebulizer/compressor in a bag about the size of backpack. I tell the TSA agent as I'm putting it on the conveyor belt that it's a bag of medical stuff, and they've been pretty good about that.
The thing they seem to be adamant about right now is that you put your laptop and camera or video camera in its own bucket as you slide it through the x-ray. I'm not sure why that is, but they were none too pleased that I set my sweatshirt on top of my lap tap. (I've only got two hands, and was just trying to expedite the whole process...)
Since you'll be bringing a note, I don't think you'll have any problems. One thing I didn't do this time that I wish I had, was wear slip on shoes or even slippers to the airport. By far the thing that slowed me down the most was taking off my shoes and putting them back on while trying to repack my laptop.
One last piece of advice (sorry this is so lengthy). If they DO give you a hard time and force you to throw away any liquid medication (like TOBI or Pulmozyme) WRITE DOWN THEIR NAME, what they threw away, and have them sign it. That way you'll have much better luck getting insurance to refill the script.
Happy travels!