I believe the setting can be changed by opening it and moving a jumper or two. 0.9V or 2.0V options are just how you want it set up at the factory.
While it is slightly different beast, I have a miniDSP 2x4 Balanced and can attest the voltage scales are easily changed by internal jumpers.
The consideration in voltage is with analog input relative to the scaled input of the ADC. For the best operation you want the incoming signal as close as possible to the max voltage, without going over.
For example, say it is a 16-bit ADC with 0.9V input scale. That means the 0V to 0.9V range will be represented by 65536 individual values (0 to 65535). As you see, to get the full resolution capability, ideally the signal would use the full range possible. Of course, if you go over then that's not good because there no more values left to properly represent the signal.
If the input is scaled to 2V, there are still the same 65536 values but each value is a bigger chunk. So, if you input only 0.9V on the 2.0V setting you'd be using less than half the available resolution.
In most cases the signal will be less than 0.9V so I'd probably start with that setting. Again, far as I know, it can be easily changed if that doesn't work out.
Potentially a bigger concern though is the 2x4 max output of 0.9V regardless of the input setting. If you have amplifier that requires more than 0.9Vrms to achieve the level of output you want the miniDSP 2x4 itself will not be capable. Bear in mind though, 0.9V into most amps would be pretty loud so it may be OK despite that limitation.