The SQLIOSim knowledge base article outlines the various configuration files in detail.  http://support.microsoft.com/kb/231619 - How to use the SQLIOSim utility to simulate SQL Server activity on a disk subsystem.

I still get inquires about what should I run by default.   My answer is:  Use the default.config.ini but update the following.

• Number of iterations  to 5 ore more
• Testing iteration duration to 300 seconds or more.   I like 600 myself.
• File(s) - Make sure the names, paths match that of the problem system and you want the size to be larger than the hardware cache.  (NOTE:  Don't specify the SQL Server .MDF or .LDF files or it will erase the database data)