In a still air, the thermometer should be at the top of the eggs. The temperature at different levels can vary quite a bit since hot air rises. The recommended temperature for a still air is 101.5 degrees Fahrenheit taken at the top of the eggs.
I follow the instructions for filling which trays when (The instructions with mine are the same as yours) and just use my hygrometer to tell me when I need to refill the water reservoirs. That is usually every three or four days with mine. I don't worry about what the readings are, just that when they start to drop, it is time to add water. I break my unhatched eggs after the hatch to see what the problems were. So far, none look like they were caused by humidity problems.
It is good to be asking questions and trying to get it right, but try to not overthink it. Most incubators work pretty well if you follow the basic instructions. Try to keep it fairly simple the first time and see what happens. If you follow a lot of different suggestions, you'll be jumping all over the place and, if you do have a problem, you won't know what caused it or how to correct it.
I know it is exciting and that you really want to get it perfect the first time. I did too. I really think the best thing to do is keep it fairly simple. If you see a blatant problem, like that 33% humidity, try to understand and fix that before you start, exactly like you are doing. You are asking good questions. I predict you will do well.
