If you mean /usr/<somenewdirectory>, yes that would be ok, thought not a good idea. It should be in /home, or /usr/local. DO NOT chmod /usr/*. You will regret it.
Right, it would be:
chmod [rights] /usr/<specifieddirectory> -R
In the future it's possible it could be moved to /usr/local, that would make more sense. at the current time it's not a simple move... although, a symlink might work ok. Might have to try that.
James