For covering the brakes, different riders do it differently, and some instructors want it done differently than others. I always keep my right foot near the back brake pedal, I use my index finger and thumb to turn the throttle, and the smaller three fingers on my right hand are for the front brake lever or throttle.
Many sportbike riders only use one finger to put on the front brake- their front brakes can easily lift the back tire off the ground. Some riders use all four fingers for the front brake, but as a former dirt bike rider I learned that this causes a loss of throttle control while and just before or after using the front brake. I only cover the front brake lever when I see traffic nearby or it is an especially tricky road, but some instructors will have you cover the front brake lever all the time, since it is safer for a beginner.
It is best to cover the brakes without touching the levers, so the brake lights do not go on too often, unless you want to give early warning to a driver behind you. You can flash the high beam headlight to warn drivers in front of you, along with the horn. I also do head bobbing and sometimes stand on the footpegs, to make myself more visible if I think a driver has their head up their ass (not paying attention).