If you need to set a flag on the apppool in server 2008 you can also do that via script. Here is an example of how to set the "Enable 32bit application support" flag to "true" in server 2008 apppool:
cd %windir%\system32\inetsrv\
appcmd set apppool /apppool.name:CPOSBackOfficeWS /enable32BitAppOnWin64:true
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