Hi! I’m an incoming freshman at UC Berkeley and I’m planning my course schedule for next year. The Plan of Study on the Berkeley website says I have to take a Natural Science Elective, and it wasn’t really clear if I could AP out of that. I’ve taken the AP Chemistry and AP Physics Exams, for example.
Could anyone explain that to me? I’m so confused. 
You’ve got an EECS plan pulled up. Natural science classes aren’t required for LSCS, though you could if you want.
For L&S, AP credit cannot be used to fulfill any of your 7 breadths. If you did get a 4 or 5 for AP Chem for example, you would be able to take the next Chem class, but by itself it doesn’t reduce a class or fulfill a requirement. But you really don’t need to go out if your way to take a Physical Science breadth class, as CS 61C (a required class for all CS majors) fulfills that requirement.
You’ll find that for the most part, the only really useful AP classes for Berkeley L&S are AP Calc and AP Lang/AP Lit, since a qualifying score gives you subject credit. The others will give you graduation credit but nothing more.
I should qualify that last sentence. If you got a 4+ in say AP Psychology, you would get credit for taking Psych 1 and be able to take the next Psych class, if you want. But it doesn’t fulfill any requirement other than an elective. Similarly if you got 4+ in both MicroEconomics and MacroEconomics, you would get credit for Econ 1 and be able to go on to the next Econ class, but once again it doesn’t fulfill any requirement, breadth or CS major or otherwise. Since Psych 1 and Econ 1 are both classes that fulfill a L&S Social Science breadth, you would think that the AP credits would suffice, but nope - gotta take an actual class at Berkeley. Or if you had credits from a CC, that would work. But not AP.
Here is a sample plan of study that you should be looking at:
https://berkeley.app.box.com/v/ugrad-sample-cs-freshmen
do note that those plans where Math 1A and/or 1B needs to be taken is pretty unaggressive IMO especially if you have a programming background. On the other hand, advisors will probably tell you to take 3 classes plus a DeCal your first semester rather than 4 classes.