I do, too!! I know that people who have incubated before normally only candle 2-3 times during the incubation process, but this is my first time in a homemade incubator, and I want to make sure things are progressing okay. I do a lot of comparisons to the candling pics on Metzers site (I've got duck eggs). I have my hands in there all of the time anyways since I have to hand turn the eggs every couple of hours.
I always wash my hands every single time I touch the eggs . Then when I'm candling the egg, it's out of the incubator for less than a minute, and handled very carefully- no bumping or shaking.
So, make sure your hands are clean (so you don't introduce bacteria to your eggs), handle them gently, and quickly put them back and get the incubator temp and humidity to the correct levels immediately after. This is what I'm doing, but seeing as how I haven't hatched anything YET, you may want to wait for someone with more experience to chime in with better advice.
Good luck with your hatch- it's exciting, isn't it?