That shouldn't really matter. When using a single channel, the volume needs to be set twice as high, which might cause some pops in the sound (if you broadcast silence on one channel, you might hear some soft pops), depending on the quality of your sound card. Two channels on the other hand might have a phase shift problem, which will cause some loss of very high frequencies (which can be repaired using the FM Calibration window).
BTW, for the Realtek card, check the help pages - there's a remark on enabling 192 kHz mode there (see
http://help.stereotool.com/fm_transmitt ... card.shtml ).