Multisite CometChat Setup Question

I am running CometChat on my sub-domain of

The cometchat folder is in my public_html folder and it takes forever to load on the main site, where it really is not needed.

I am wondering if I can put cometchat folder in my /mary-content/uploads/sites/2/ folder and delete it from my public_html folder or will that break my website/chat rooms?

Will that stop it from trying to load on the main website?

So then, do I create a new header.php in the site/2/ folder for the cometchat script?

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