File Manager for Subdomain

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Hi
I've installed a second copy of C5 (8+) in a subdomain in my public html folder on a CPanel using host. it's set up like "subdomain.mysite.net". I also have my regular domain set up "mysite.net" for my regular site the file manager works normally. For my subdomain the file manager is not working properly, I only see broken image icons instead of the actual images when using file manager an they won't work for a content block. I've tried changing the default file path to various things
/home/mysite/public_html/subdomain/application/files/tmp
/home/mysite/public_html/subdomain/application/files/incoming
I believe I may have to edit the php.ini file of the dispatcher file to get it to point to the proper place.
Interestingly when I chose to view a file in file manager i can see that image. So i think i'm close but if anyone has any experience with this i'd appreciate it.