I went and checked on this via FTP at root a couple hours ago and discovered it was all listed as belonging to root, which was strange because it was installed for a specific user. Now I've changed it to reflect the user and site etc. it seems to be working much better and I was able to make some changes.
There are still a few points I need to work though like just receiving a message saying that I need create a .htaccess file for the permalinks to work and again saying I haven't allowed permission. I'll work that one out somehow.