The domain certificate is always installed in IIS. If it is installed using the Certificates snap-in of MMC then it frequently breaks the key pairing of the certificate and the private key.
When you import the Intermediate certificates using the Certificates Snap-in of the MMC it automatically places these files in the right certificate store. So it doesn't really matter where you try to install them, they will always go to their intended store.
When you import the Intermediate certificates using the Certificates Snap-in of the MMC it automatically places these files in the right certificate store. So it doesn't really matter where you try to install them, they will always go to their intended store.