Do you want to use different web.config in the website folder?
For example we want to use a different app key value in a subfolder code file but we already have the same name key in root folder web.config.
For Example
Root web.config
<add key="examplekey" value="123" />
Sub-folder web.config
<add key="examplekey" value="456" />
If your sub-folder code files don’t have web.config then it will continue to use root web.config value.
So in order to have Sub-folder its own web.config and key then you should follow following instructions
In the root’s folder web.config wraps the <system.web> element with the following element: <location path=”.” inheritInChildApplications=”false”></location> and leave all other settings/elements unchanged.
For Example
<location path="." inheritInChildApplications="false">
<system.web>
</system.web></location>
In sub-folder web.config only have the following
<?xml version="1.0"?>
<configuration>
<appSettings>
<add key="examplekey" value="456" />
</appSettings>
<connectionStrings />
</configuration>
This way you sub-folder code file will start using new value from the sub-folder web.config
We also like following article on sub-folder web.config
https://techcommunity.microsoft.com/t5/iis-support-blog/how-to-prevent-web-config-files-to-be-overwritten-by-config/ba-p/297627
Read more about IIS settings https://blog.certificationskart.com/category/windows/iis/