Dark Andy, the Instrument Amp is not an INPUT, it is an OUTPUT option. The Duet has four inputs -- 2 Hi-Z Instrument inputs, and 2 XLR inputs. I can easily record my amplifier with my SM 57 and the XLR input. After doing so though, I was thinking of reamping with one of the two output. With Maestro (which comes with the Duet), I am able to change the output from 'line-out' to 'instrument amp.'
I am not sure what the exact function of the Instrument Amp option is, but I am guessing it is for reamping or using you Duet and amp as a monitoring system. I am not entirely sure though, hence why I am on here asking advice. I would just call Apogee, but it is the weekend, and a three-day one.
Thanks though.