I recently had to move some folders to my home directory on my Debian GNU/Linux 6.0 installation as the root user and I then had to change the ownership of the folders and the files within to my current user.
For example I copied the ~/.themes folder to my home folder and I had to change ownership to myself, so I used this command to change ownership to the lovecraft group which my user is a member of:
root@Shothoth:/home/lovecraft# chgrp -R lovecraft .themes/
Then I had to change ownership of the files to my user:
root@Shothoth:/home/lovecraft# chown -R lovecraft .themes/
After these two commands executed as the root user the folders and files belong to your user and you can get access to them without any problems. That is how simple it is to move folders to your home directory and change the permissions and ownership of the files. Type
man chown and
man chgrp to get more information.