Replacing SHA-1 certificate with SHA-2

We have a certificate that needs to be replaced. It is currently SHA-1, and we wish to replace it with SHA-2. We created a new certificate request and have received the replacement. The Root certificate remains the same; we now have two intermediates, instead of the one for SHA-1; and we have a new certificate with the same CN. Server is running Windows Server 2008 R2 and IIS 7.5.

1. Should I remove the existing intermediate and server certificates before adding the new ones?
2. Can the two intermediate certs be imported in a single file, or do I need to import them individually?

Thanks,

  John