I can pass on a couple of thoughts from my travels. CPAPs don't count as part of your carry on....they are medical equipment and in my flying since I began treatment I've never had an issue. Do keep it separate....just like a laptop, they like to x-ray it separately to make sure you aren't hiding anything in it.
Suggestions to make life easier:
1) Let the airline know in advance that you are bringing your CPAP regardless of whether you need to use it on the flight or not. They are usually quite discrete and it saves some over-enthusiastic flight attendant getting mad at you thinking you have more luggage than you are allowed.
2) If you have time, you can get or make a tag for the CPAP carrying case (there are lots of pics online to give you ideas) that identifies it as medical equipment. Security has seen enough of them and even for the newbie screeners, it means less questions.
3) Your water (if you choose to bring distilled with you) is also exempt from the container rules...just make sure that you declare it when you get to security. I have some medicine bottles from my local pharmacy (1/2 quart / 500 ml ones) that use. I put identifying stickers on...distilled water, for CPAP etc....and the worst any screener has done is swabbed them for explosives testing.
4) Pack your mask in a clear ziplock. If they want to open the bag and handle it at all, you are well within your rights to ask them to put on a fresh set of gloves before they do.
5) Relax. The airlines and security have seen CPAPs before and it'll be more new for you than them