When I have to get up, I like to take a deep breath, manually turn the machine off, and then take off the mask, but this is mainly just to prevent the loud sound of air blasting out of the hose, which would disturb my wife. This also makes your data more accurate and indicative of what's going on during the night. If you left it on, it would be logged as a large leak for a couple of minutes while you're in the restroom.
As for your score, don't worry too much about the mask on/off events. They are basically arbitrary metrics that ResMed decided to include in its "score" scheme. The only MyAir metrics that really matter are usage hours, AHI, and perhaps leak. If you're worried about insurance tracking your compliance, they basically only look at usage hours.
As you have already heard, it is highly recommended that you download SleepyHead and start learning how to track your own therapy, since MyAir provides only the most basic, high-level overview. That's what this board is all about, and I think you'll find it's a lot of fun too, particularly if you're a scientific, data-oriented person (i.e. a nerd).
