Pages 121 and 125 of the reference manual describe the relevant settings. I would start with the pre-programmed templates "MIDI Pedal 1" or "MIDI Pedal 2." Some experimentation is required.
Your keyboard has four real-time parts (R1, R2, R3, and Left.) If you're trying to use it like an organ, you would probably activate at least one RH part representing the upper manual, a left part representing the "lower" manual, and the bass part played by the pedals. You'll have to specify the pedals' incoming MIDI channel as the bass note.
I'm sure that there's a way, using MIDI, to map the incoming pedal notes to trigger the R2 or R3 voice, which would give you full latitude to choose and modify the voice. If not, there's another workaround...
I believe Yamaha's intent is that the pedals would control the STYLE bass note. With the style running, the bass follows a pre-programmed pattern, transposed according to the pedal pressed. However, for an authentic organ experience you might play chords with ACMP on, and the style STOPPED. This is called "Stop Accompaniment."
By default, you'll hear a relatively quiet monophonic bass and a string pad. But there's a way to configure the accompaniment so that instead, you'll hear the voice assigned to the bass and pad tracks of the STYLE. Most often the bass voice will be an electric guitar or a stand-up bass. These have a sharp attack, but lack the ability to "sustain." Revoicing the style bass to an Organ tone or something in the Strings family might be more suitable. The last step is to mute the pad voice so that all you hear from the style engine is the bass.
Now when you play, you should hear the "Left" and "Right" voices on their respective sides of the keyboard. And when you play a pedal, you'll hear the style bass voice you specified. This should give a pretty faithful emulation of a two-manual home organ.
I hope this helps. You'll have to experiment, and I also suggest that you search the forums on psrtutorial.com. There are a lot of Yamaha experts (and former organists) who post there, and have probably done exactly what you're trying to do.