I'd do a little different.
ee site create as usual
domain.com in your new hard drive:
mv /var/www/domain.com/* /data/var/www/domain.com/
rm /var/www/domain.com -rf
ln -s /data/var/www/domain.com /var/www/
The symbolic link will make everything work as if the website was configured on default location, while it's files would be actually stored wherever you want.