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One question – How are the external drives attached – USB 2, USB 3, eSata, FireWire (IEEE 1394), etc…?
I am assuming SATA 3G but 6G would be better for the internal.
As a rule, you would want the externals on different data paths – i.e. eSata for the big one and USB3 for the smaller.
You also don’t mention what speed (or make/models) the drives are – The faster the RPM and bigger the cache, the better your response times will be.
I would store the source video on the internal, additional assets (music, graphics, etc…) on the faster of the externals and render to the slower of the externals. But that’s just me. Your mileage may vary and I don’t know many of the specifics of your setup.