I am MDA certified but got Keiser certified as well since we have those bikes at one of the clubs that I teach at. They are wonderful bikes and apparently much research/improvements were done compared to the last model. There was much debate regarding if they were going to put the 'aerobars' on these bikes, and obviously it was decided that it was a good idea.
Personally, I don't use them (even though I am a triathlete), and I ask/plead/request that my students don't use them either. Sitting in an aero position (when not properly conditioned/set up properly) puts immediate pressure/compression on the lower back, causes you to collapse onto the handlebars- impairing your breathing, and very simply, you don't 'need' to be aero in an indoor class (no wind ). This being said, I always say that if there are those in class who are experienced riders whose bodies are used to being in this position and they are set up for being in this position...then it is fine by me how they ride (I always give my riders the saftey info, dos and don'ts and let them make the judgements for themselves). Typically, when a rider is in the aero position (as in triathlons) the setup of seat position and pedals is different from regular road riding. That is why there are road bike and Tri bikes.
ANYWAYS, I don't think there is a proper way to use this part of the handlebars in an indoor cycling class,b ut you always have those who ride on them the whole time. The best we can do is to educate on the contraindications, benefits of riding with proper form and then let them ride how they see fit.
Hope this helps!