You merely need to rest the eggs on the incubation medium. Certain species of turtle require the eggs to be buried in the substrate, notably matamata eggs (they require an acidic incubation medium that will eat away the outer layer of the shell, making it easier for the hatchling to emerge at the end of the incubation period), but I have never used this method for tortoises. Ensure reasonably high humidity, 60 to 90% (tortoise eggs tend to be quite adaptable in this regard, though tropical forest tortoises are the exception).
I've never used a sharpie in marking eggs. I always use a pencil, as it leaves minimal graphite markings. I don't know what the effect would be. Best to just wait and find out, unless someone else on the forum has some experience in this regard.
As far as the temps go, some fluctuation is okay. I wouldn't allow the temp to get below 82 or above 90. I've seen the effects of both extremes. My first clutch of russian tortoise eggs was a miserable failure. I collected them and tried to incubate them in my closet, which had an average temperature of seventy eight. All four eggs failed to develop. On another occasion, I had a hovabator heating unit malfunction (luckily I had bought a spare!), sending the temperature around 95. It was only for three hours, but the hatchlings that resulted had extra scutes and two of the five (the least robust hatchlings) died within one week of hatching. If you are to mimic wild conditions, have fluctuations coincide with daytime/nighttime changes (i.e. warmer in the day, cooler at night). Some keepers argue that these natural fluctuations produce tougher hatchlings. I choose to remain skeptical until some statistical data is presented to prove the point. Good luck with your eggs, and remember that they won't hatch at the same time unless you're exceptionally lucky. Sometimes, months can go by between the emergence of the first and last hatchling. I remember my first russian hatchling, though. I was so excited when he emerged from the shell, and so was he! After I'd given him time to absorb his yoke sac, I reached for him to hold him in my hand for the first time. To my surprise, he dashed from his shell and made it across the eight inch incubation container in a second, looking to escape me.
T.G.