Thanks! I resolved the latest problem (section numbers) with your updates.
But I met another problem!
When I make citations using Papers 3 which have "&" and export PDF via LaTex, I can see the error "Misplaced alignment tab character &" after clicking eye that appears on lower-left side.
For example, let's say I have following sentence in the paragraph:
Blah Blah Blah (Apple & Boron 2015) Blah Blah~~~
It only happens with reference with two authors which appear like "Apple & Boron".
If I have only one or more than two author, like "Apple" or "Apple et al.", it is okay.
I am using MacTex.