Hi Yulstar,
You only need to change your config.php. I would recommend putting your site into maintenance mode whilst you perform the move. This will ensure you don't miss any files by mistake.
As Visvanath has already aluded to, /usr is really the wrong place for data. Yes, even /usr/local. The correct place according to the File Hierarchy Specification is /srv - see http://www.pathname.com/fhs/pub/fhs-2.3.html#SRVDATAFORSERVICESPROVIDEDBYSYSTEM for information. It's up to you how you arrange it but I'd advise something sensible which states what it's for. I would recommend something like /srv/www/URL/data. For example:
/srv/www/moodle.org/data
Your file permissions must stay the same, so I would recommend using rsync. I would recommend against using cp or mv. If you have to interrupt the transfer part way through, you will have to start again with a cp, and mv will not be atomic across file systems. rsync is designed for this kind of purpose and can be invoked with something like:
rsync -avi /usr/local/somewhere/really/strange /srv/www/my.moodle.site/data
Best wishes,
Andrew