Config files inherit their values as you move down in scope (server -> site -> application), but by default it's only for specific sections. The IIS site has an article on the ApplicationHost.config file as well as configuration delegation.
As an example, there are two different requestFiltering sections within applicationHost.config: one for an FTP server and one for web sites. You can see how the section for web sites (system.webServer) allows the values to be overridden:
<section name="requestFiltering" overrideModeDefault="Allow" />Whereas the section under system.ftpServer does not.
<section name="requestFiltering" overrideModeDefault="Deny" />So, onto your question. You should be able to update the Web.config to modify the allowed content length for your site (and sub-sites), unless you have changed the overrideModeDefault value in your applicationHost.config.