I read somewhere you should use commas instead of brackets/parentheses, but my sentence doesn't really make sense with commas

"Whilst the two concepts remain distinct (eating more chocolate does not necessarily mean you are obese), they are mutually influential"

just to add my study isn't on chocolate! (wish it was)

I would have thought you were fine to use brackets - I've certainly used them in my work and I've seen them in various theses I've read so I probably wouldn't worry!

:-) Mmm...I wish my thesis was on chocolate too...with lots of taste tests!!!

I think it should be fine so long as you use them consistently.