The IIS 7 manager provides a UI for almost all sections for the web.config. It does simplify things for administrators but I have seen a couple of cases where this has lead to interesting problems.
Let us consider the Machine Key feature that the IIS 7 manager provides. It is well known that when you deploy your web application across a web farm you have to hard-code the machineKey section of the web.config on all servers so that they carry the same keys that are used for encryption/decryption. The IIS 7 manager also has a useful option to generate random keys.
If the keys are not synchronized across all the web servers you can expect authentication or viewstate issues. One of our customers was well aware of this and had hardcoded the machineKeys using the IIS 7 manager. Yet he was facing all the issues related to the machineKeys not being in sync’.
After a lot of troubleshooting the issue came down to the bitness of the worker process.
Read more here http://blogs.msdn.com/webtopics/archive/2009/12/04/64-bit-iis-manager-32-bit-worker-process-and-root-web-config-settings.aspx