if your using an onkyo receiver or pre-amp you should use either Direct or Pure Audio (pure audio is engaged via a button on the receiver/pre-amp front face) this bypasses all processing and should give you signal straight from your input either into the receivers or pre-amps DAC or if you are using your transports DAC then the signal in your receiver or pre-amp would then go straight out to the amp via said pre-outs.
for LFR purposes, i'd recommend setting them as large or full range. they got broad shoulders and can take it! happy dishing!