This is a handy trick for if you really want to have your files in one place but accessible everywhere.
I did this on my server because I felt things were getting fragmented between my various home directories and files I had on my ownCloud.
So to keep everything in one place I created a symlink from the home directory on my server to to the /owncloud/$USER/files directory.
ln -s /home/$USER/ home
You need to grant apache access to the files so:
sudo chown -R www-data:www-data /home/$USER
and then add your user to the www-data group (for me on my server this was root):
sudo adduser $USER www-data