You can select Through Mode (THR) from a drop down menu in the top left corner of the Virtual Deck area. THR mode mutes the selected deck. When a channel is set to software THRU, the corresponding virtual deck display will show as THRU mode and waveforms will be greyed out. Audio on that channel will bypass most of the audio processing units, with the exceptions of FX and the SP-6. Transitioning from ABS/REL/INT mode into THR mode will pause the current song on the corresponding virtual deck but all other states (e.g. loops, key lock, etc) will be preserved.
Software THRU gives you the ability to apply effects and/or drop samples to the input source (e.g. analog vinyl).