I have a similar setup. When setting up the mount point in nitoTV for the AirDisk use smb and the auto option (that will automatically mount the Airdisk under Movies).

As far as reference movies go I do this all the time but it's a bit more complicated than QTPro. The easiest way is to use VideoDrive (option 4) which creates a mov container with the avi file inside and tricks iTunes into thinking it is H264. You can also add Metadata. There are free solutions but those are a bit tricky. VideoDrive will do what you want.

ls