When you install EX specify a UNC path to the NetApp for the container files. If you've already installed EX launch EX Admin, right click the computer object, select properties and change the path. You'll need to copy any existing container files to the new path and restart the services.

Thanks for the info. But I'm also planning to use the NetApp box for the EX installation/message centre drive, the SQL database and the the EX indexes. Can I mount these drives from the NetApp box to the EX server as NTFS drive letters?

I'm not sure. This sounds like a NetApp question.
The important thing to remember is that it must appear as a locally attached drive to be used by SQL and the Message Center. Having said that I suspect using a NAS device for either the SQL data files or for message processing is probably a bad idea.
Hope this helps.

Thanks for that. Are you saying it's a bad idea to use a NAS box in the manner I've described because I need to ensure the drive mappings remain persistant?

I think my main concern is processing a large amount of data over ethernet. I have no experience using SQL or EX in the manner you described however it might work fine assuming you can make the resource appear as a local drive letter. Please let me know if you get it running.