How to make a change in iis apppool using appcmd.exe

I never use appcmd.exe but you could do this:

 appcmd.exe set config  -section:system.applicationHost/applicationPools /[name='DefaultAppPool'].enable32BitAppOnWin64:"True" /[name='DefaultAppPool'].managedPipelineMode:"Integrated" /[name='DefaultAppPool'].startMode:"AlwaysRunning"  /commit:apphost
 appcmd.exe set config  -section:system.applicationHost/applicationPools /[name='DefaultAppPool'].processModel.identityType:"LocalSystem"  /commit:apphost

In PowerShell using the WebAdministration Module:

 Set-WebConfigurationProperty -pspath 'MACHINE/WEBROOT/APPHOST'  -filter "system.applicationHost/applicationPools/add[@name='DefaultAppPool']" -name "enable32BitAppOnWin64" -value "True"
 Set-WebConfigurationProperty -pspath 'MACHINE/WEBROOT/APPHOST'  -filter "system.applicationHost/applicationPools/add[@name='DefaultAppPool']" -name "managedPipelineMode" -value "Integrated"
 Set-WebConfigurationProperty -pspath 'MACHINE/WEBROOT/APPHOST'  -filter "system.applicationHost/applicationPools/add[@name='DefaultAppPool']" -name "startMode" -value "AlwaysRunning"
 Set-WebConfigurationProperty -pspath 'MACHINE/WEBROOT/APPHOST'  -filter "system.applicationHost/applicationPools/add[@name='DefaultAppPool']/processModel" -name "identityType" -value "LocalSystem"

in both cases you need to replace the name DefaultAppPool with the real name.

I hope you have very good reasons to run your pool as System, I would never do that.