Yes, or perhaps I should say, most likely. If you have two software synthesizer Virtual Instruments (VI's) you can filter out data that you do not want to be sent to them. Go to the
effects window, select the first VI, then click on the MIDI cable icon. This brings up the
Effects MIDI filter and options dialog. Deselect the channels that you do not want to receive MIDI on. Do the same for the second VI.
The only case where this would not work would be if both VI's were so inflexible that they will only respond on one MIDI channel and it is the same MIDI channel.