Configuring MySQL (my.cnf) for MyISAM and InnoDB
You mentioned before you are running

MySQL 5.5.29
16 GB RAM

Here are some good settings to start with
innodb_buffer_pool_size=4G
innodb_buffer_pool_instance=2
innodb_read_io_threads=12
innodb_write_io_threads=12
innodb_io_capacity=300
innodb_log_file_size=128M

Don't do the conversion yet !!!
Put there settings in my.cnf, then do the following
service mysql stop
cd /var/lib/mysql
rm -f ibdata1 ib_logfile*
service mysql start

Now, you can do the conversion.
Give it a Try !!!
UPDATE 2013-05-10 10:44 EDT
Here are my past posts on tuning InnoDB for better CPU usage

May 26, 2011 : About single threaded versus multithreaded databases performance
Sep 12, 2011 : Possible to make MySQL use more than one core?
Sep 20, 2011 : Multi cores and MySQL Performance

Here are my past posts on tuning InnoDB

Feb 16, 2011 : How to safely change MySQL innodb variable &#39;innodb_log_file_size&#39;?
Apr 14, 2011 : What are the main differences between InnoDB and MyISAM?
Mar 25, 2012 : Why does InnoDB store all databases in one file?
Oct 22, 2012 : How large should be mysql innodb_buffer_pool_size?