I have found this to be the case in my IncuView as well and I do rotate my eggs to make up for the temperature variation in the incubator. It's one of my biggest complaints with the IncuView but it's pretty standard in many incubators unless they have a turner that goes all the way around the incubator. Other than being a bit dryer than my other incubators the IncuView is still one of my favorites. Good luck on your hatch!
EDIT to add, yes I would leave it at 99.5°F unless you find that it's predominantly low in most spots. I mapped out the entire incubator and I do have a corner that occasionally drops to around 98.9 and another corner that gets as high as 101.2 but most of the incubator reads at 99.5 to 100.