Multiple SQL Server Integration Services (SSIS) database instances on one machine

The registry key
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\MSDTS\ServiceConfigFile specifies
the location and name for the configuration file that Integration
Services service uses. The default value of the registry key is
C:\Program Files\Microsoft SQL Server\90\DTS\Binn\ MsDtsSrvr.ini.xml.
You can update the value of the registry key to use a different name
and location for the configuration file.

Reference: Multiple SQL Server Integration Services (SSIS) database instances on one machine - Mike's Blog