Fiddler is a proxy. It works by changing your system's proxy settings to point to itself. By default, it automatically chains to the system's upstream proxy (see Tools > Fiddler Options > Gateway) and forwards requests to the system's proxy, which means your scenario should work just fine.
Now, I think you're saying that you're relying upon an INS file instead of a proper PAC (proxy autoconfiguration) script file. INS is not supported by most of the HTTP stacks on Windows (WinHTTP, System.NET, etc) which means that Fiddler will not chain to the proxy specified inside the INS file and will instead ignore it; you should see a remark about this in the LOG tab when you start Fiddler.
To workaround this, you can manually specify the proxy configuration to which Fiddler should chain using the aforementioned Tools > Fiddler Options > Gateway tab, and you should encourage your IT department to move off of the deprecated INS configuration feature and instead use a PAC file.