Difference between root/templates and root/lib/pkp/templates?

Hello I would like to know what is the difference between templates folder in root of website and templates in lib/pkp. I want to change templates and css and I am a little confused.
Thank you in advance.

Hello, see if this part of the documentation helps clarify:
https://docs.pkp.sfu.ca/pkp-theming-guide/en/html-smarty