I know its possible to backup individual schemas with innobackupex but how do you restore an individual schema without affecting the others? Do I just copy the backup directory structure and files into the working mysql directory?
For MyISAM yes, but for InnoDB see http://www.percona.com/doc/percona-xtrabackup/innobackupex/importing_exporting_tables_ibk.html
The process depends on if you are using MyISAM or InnoDB/XtraDB, but below are links to the manual with important information and steps on both taking the partial backup, preparing it, and restoring it:
thanks for the info. very helpful