There are additional steps to do this if you've used innobackupex and followed the steps on section "Create the Backup" and "Prepare the Backup" under www.percona.com/doc/percona-xtrabackup/howtos/recipes_ibkx_l ocal.html

After preparing the backup, just edit your my.cnf config file to the log file settings that you would like to use and then move or remove the ib_logfile(s)(Eg. mv /data/backups/2010-03-13_02-42-44/ib_logfile* /root) stored in the backup dir.

After that restore the prepared backup to the MySQL datadir as discussed in the "Restore the Backup" section. When you start MySQL, the log files will be generated based on what you've set on my.cnf. You can view this from MySQL error log.

Here's a sample of the log:
130313 4:30:35 InnoDB: Log file ./ib_logfile0 did not exist: new to be created
InnoDB: Setting log file ./ib_logfile0 size to 512 MB
InnoDB: Database physically writes the file full: wait...
InnoDB: Progress in MB: 100 200 300 400 500
130313 4:30:43 InnoDB: Log file ./ib_logfile1 did not exist: new to be created
InnoDB: Setting log file ./ib_logfile1 size to 512 MB
InnoDB: Database physically writes the file full: wait...
InnoDB: Progress in MB: 100 200 300 400 500
130313 4:30:49 InnoDB: Log file ./ib_logfile2 did not exist: new to be created
InnoDB: Setting log file ./ib_logfile2 size to 512 MB
InnoDB: Database physically writes the file full: wait...
InnoDB: Progress in MB: 100 200 300 400 500
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
130313 4:30:54 InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
130313 4:30:54 InnoDB: Started; log sequence number 0 571354124