What I'm doing and yes I'll have to double check permissions on files and folders, as my web host doesn't need those two folders to be 777, they can remain 755 and it will change permission auto itself on install for folders and files inside them to 777. I'm uploaded one level above ROOT and then I'll copy Chmod permissions over before deleting that public_html folder and renaming the one I'm uploading the same name to take it's place before uploading the upgrade files. I didn't want to risk uploading to that public_html folder again because I wasn't sure how much difference there is between the older version I uploaded by mistake (files no longer used and removed maybe) e.t.c?
I'm doing it the hard way, but I want to be double sure I don't have any folders using 777 that don't need to be. My server for some reason doesn't need you when installing forum software for the first time to Chmod anything, it does it auto itself, but unlike some servers that require "internal_data" to be 777, mine doesn't and instead leaves it at 755 but changes permission on folders and files inside it to be write-able.