Site in subdirectory, now Google Analytics not working

I built our website in https://www.domain.com/site
However, I wanted our URL to point to that directory without showing the subdirectory, so I used the instructions here:
https://codex.www.ads-software.com/Giving_WordPress_Its_Own_Directory
for “Using a pre-existing subdirectory install.”

Then our Google Analytics stopped working.

I am not sure if we should use https://www.domain.com or https://www.domain.com/site in Google Analytics account.

Or will GA not work at all since I essentially masked the subdirectory?