The process is quite straight forward and simple.
If you are hosted with us:
1) Log to your server using SSH
2) Execute the following software (it is installed with our servers):
fixpermissions
If you are hosted on your own dedicated server
2) Point yourself in your Apache folder (at the root of your website)
3) Run those commands
find . -type f -exec chmod 644 {} \;
find . -type d -exec chmod 755 {} \;
chmod 550 pear
chmod 550 mage
And the last bit: QA!
4) Visit your Magento's install and see if everything still run smoothly
And that's about it!