In v.2, it was possible to select (by clicking a checkmark box) those documents that you wanted to be included in Compile.
I can’t find this functionality in 3.0.
Admittedly, Compile in 3.0 is a feature I have struggled with from the beginning.
Can someone tell me where this is hiding?
If you look at the first screenshot in JoRo’s post, you’ll see a page symbol with a tick along the bottom tool bar of the editor. That’s another option that can be used to toggle documents on or off for compile purposes while you are actually working on them.
Simply piggy backed on your original post 
I like the bottom tool bar option, because I typically have the inspector open to Notes