Media should not be stored on the system drive.
I have external ( fast, raid, thunderbolt and FireWire, not USB) drives.
The avid media folder is at the top level where it stores imported, consolidated or transcoded mxf files.
I usually store xdcam and P2 card folders in their own folder and AMA access from there, some times is more successful than trying to access directly from the camera.
From there you can consolidate or transcode to an avid codec if you want.
Steve