Personally, I would not edit a single one, but instead modify the web.config files at the site or application level.
You should be able to change the httpRuntime and connectionManagement parameters this way, but not the processModel , which can only be used in machine.config.
However, you may not need to change the processModel if you are on Windows Server 2003.
As others pointed out, if you want to change machine.config, IIS6 will work in 64-bit mode by default, so that the version is editable. If you need to run 32-bit mode (for example, because you need to use 32-bit native DLL files), you can configure 32-bit mode as follows:
cscript.exe adsutil.vbs set W3SVC/AppPools/Enable32BitAppOnWin64 "true"
See this TechNet article for more information.
Joe
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