IIS 6 typically uses a standard Windows account called 'Network Service' to execute ASP.NET code. This implies that if you want QBO configuration pages to save changes to the file system, the Network Service account needs write permissions to the subject files.
IIS 7.5 and later gets a bit trickier, though more secure. By default, each Application Pool executes under a virtual account (e.g. 'IIS APPPOOL\ASP.NET v4.0'). Just like with Network Service, you will need to explicitly grant permissions to this account to write to the configuration files. However, the subject account is not listed under the list of user accounts. (It's a, ahem, virtual account.) No matter, simply type the name into the Select Users or Groups permissions dialog, and Windows will accept the virtual account name.