As far as I know, you will need to specify one channel per midiout.
To route between two programs on the same machine try LoopBe1(windows only i think) from http://www.nerds.de/en/loopbe1.html
I use it in some kiosks with heavy use. Free for non-commercial application.
It sets up a virtual MIDI driver which you can select as a MIDI out device in PD, and I assume a MIDI In for fruity loops.
I know it works with PD, Director(with MIDIioXtra), and Reason 4.
However, I have had trouble with it if using the midiout object. Works fine with noteout, ctlout, etc.