Question regarding Rate of Photosynthesis AP Biology Lab
Your task is to determine how light intensity and wavelength affect ATP production. Therefore, we know for sure that your dependent variable (or response variable) should be ATP production. It is customary to depict the response variable on the vertical axis (Y-axis), so let's trying doing this.

Now we need to sort the other two variables. I suggest that you make one variable a control variable -- a variable that you don't change and keep constant, and the other then will be an independent variable (or explanatory variable). Then you swap them around, producing at least two plots.

In a nutshell:  


You pick one value of wavelength and don't change it. Then you change the light intensity and record ATP with constant wavelength. You plot ATP (vertical axis) vs the light intensity (horizontal axis).
You pick one value of light intensity and don't change it. Then you change the wavelength and record ATP with constant light intensity. You plot ATP (vertical axis) vs the wavelength (horizontal axis).


Make sure to generate enough data points in order to be able to fit a smooth curve.



Another option would be to make a 3-D graph, with 3 axes: Y for ATP, X for wavelength and Z for light intensity. Initially, this might seem like a better approach, however 3-D graphs are not very common in science, and maybe there is a reason for it. Your goal is to make your data intuitive, easy to read and straight to the point. Science can be rather complex even without additional effort to complicate it with confusing graphs.

I would try it out as well, and see which one of two approaches shows you the trend more clearly. If I had to pick one straightaway -- I would probably go with the previous option that included a control variable.