When I am plugging my bass guitar (a Sterling RAY 35) into the MOD Duo I have to select the "low" input stage and select the lowest input setting (all way back to -12).
Minor nitpick: someone else already said that the definition of the input stages is not too clear, but I suppose the "low" input stage is the one with the highest attenuation (for hot signals).
But even then it is possible to clip the input stage of the MOD Duo. And I didn't even use the onboard EQ.
I don't know if this is possible to change, but for me the input stages are too sensitive (even in the highest setting).
On the other hand the output stage is not very hot if I try to drive a power amp (but maybe it would work better for me with a nice limiter or compressor plugin)
I am normally using this bass and the power amp with an analog preamp (Aguilar Tonehammer) without any problems. Before that I've used a Sansamp RBI and didn't have any clipping problems (on the input and the output stage).
Maybe a signal meter for the input signal (or a generic signal meter plugin) would be nice (something a little bit more granular than the clipping lights)