proper procedure to change the innodb_log_file_size is to shut the database down, change the size, remove the old log files (ib_logfile0/ib_logfile1), and then restart the database. if the log file sizes don't match it won't start back up.
it is a good idea to do this as the default is tiny and you'll reduce both your write i/o and cpu utilization. as you increase this number startup times will increase, so you probably don't need to push this beyond 256M and you should monitor and actively tune it if you think you need to go higher.
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