Is it possible to use the djm 350 only with a dj software program and still be able to use it's functions?

no reason why not

if you have a soundcard with dual stereo outputs then you can have 2 channels.(loads of dual stereo soundcards, from cheapies from numark and the likes, to more expensive/proprietary soundcards from native instruments etc)

the usb on the djm350 is for recording mixes to usb


keep in mind that you may still be interested in having a hardware controller for using your dj program(cueing, beatmatching etc)