it might be in /usr/www/html/usr/bin or /usr/www/html/usr/local/bin
try "whereis mv"
you will need to edit your $PATH so that bash looks for your executables in the correct place. In ~/.bash_profile , ~/.bashrc or /etc/bashrc (I guess that's /usr/www/html/etc/bashrc)
you will also need to edit /etc/ld.so.conf (/usr/www/html/etc/ld.so.conf) and put the correct paths to your libraries (just put /usr/www/html in front of all of them)
I really don't think it was a good Idea to do all of that though. First of all, you now have two copies of everything that was in /usr... you have the same /usr and also have /usr/www/html/usr . Why did you do this?
ooh well, I hope this helps you out