If you are running them as jobs then you dont need to do anything to the configuration files. Just ensure that the SSIS service is started on both machines, no need to set them up as a clustered resource. The SSIS service needs to be on both so that you can save packages to MSDB, but once the job is setup it runs the package via DTSExec.exe which is independent on the SSIS service.

The only time you would want to change the config file is if you wanted to connect to the SSIS service via SSMS to be able to see the stored packages.