Hi Ashton780,
You are doing this experiment, correct?
https://www.sciencebuddies.org/science- ... #procedure
This experiment doesn't have an independent, dependent, and controlled variables in the same way that some other projects do.
You are correct that the frequency of the waves being emitted by the microwave is a constant (or controlled) variable. Anything that you keep the same throughout the experiment is a controlled variable. So, if you used the same plate, used the same microwave, and used the same type of eggs for all of your trials, then those would also be controlled variables.
If you are doing the experiment as written, then you aren't changing the spacing of the eggs. However, the distance between the cooked spots of the egg white is responding to the electromagnetic radiation being emitted by the microwave. So, the distance between cooked spots is your responding (dependent) variable, rather than your manipulating (independent) variable.
The manipulating (independent variable) is a bit ambiguous in this project because you don't really change anything. The cooked spots are responding to the electromagnetic radiation, but you don't ever change the electromagnetic radiation you submit the eggs to (assuming you cook them all for the same time). Maybe the clearest way to express this is to explain that you are trying to characterize the electromagnetic radiation that the eggs are responding to.
We'll see if any other Experts chime in with their thoughts on this. Post back as you have other questions or if you need some clarification. I would also suggest talking with your science teacher about this.