Giles -
It's not how I'd lay it out ...
For applications (SQL, Exchange, Sharepoint) we'd typicaly create seperate storage for the data seperate from the host VMs.
This storage would be LUNs presented to the VMs rather than using VHDKs.
I might create several SVMs(vservers) with multiple volumes and multiple LUNs.
A vserver for HyperV with two volumes and LUNs - one for the desktops and another for the application server VMs.
A vserver for SQL with volumes/LUNs for data Files, logs, System DB. Optionaly dedicated LUNs for data and logs if multiple DBs are being served.
A vserver for Exchange with multiple volumes/LUNs.
A vserver for Sharepoint with multiple volumes/LUNs.
This is the short answer.
We take days to teach application configuration in our HyperV, MSSQL, Exhange, etc. on NetApp courses.
(Would love to see you in class!)
You may want to view some of the Web based training on these applications available on learningcenter.netapp.com
There are also a number of Best Practice TRs on setting up these applications you may find in the NetApp library: http://www.netapp.com/us/library/index.aspx
I hope this response has been helpful to you.
At your service,
Eugene E. Kashpureff, Sr.
Independent NetApp Consultant http://www.linkedin.com/in/eugenekashpureff
Senior NetApp Instructor, FastLane US http://www.fastlaneus.com/
(P.S. I appreciate 'kudos' on any helpful posts.)