You can get different kinds of organ sounds with one, two, or three RPs.
If you have one RP: use one of my patches with a rotating speaker effect, a phase shifter effect, or a univibe effect. Work the pedal to make the rotating speaker sound speed up and slow down. If you can, use both left and right outputs into a stereo PA–the spatial quality it gives to the rotating speaker effect is amazing.
If you have two RPs: Put the rotating speaker effect on one, and run the output from that RP to the input of the other. On the second RP, use my 8+16U patch, which gives you an octave up plus two octaves up, under footpedal control, with no amp modeling. This is a sound that cuts through a mix, especially the double octave up setting.
If you have three RPs: Put the rotating speaker effect on one, and run it in parallel with another running a low octave patch (i.e., send the outputs of both devices to a mixer to be mixed into one signal), like the FBD8D or FBA8DW patches. Take the mixed output and put it through the third RP, again running the 8+16U patch. This sound has a lot of octaves in it, and it’s big and very organ-like.
Here are a couple of clips of organ-style leads that I played using a three-RP setup. Both were improvised over the same 3 or 4 layer harp loop, played on a B Dorian Minor harp in second position (f# minor). The first is a very rock-organ sound; the second is a dreamy Lowry organ style lead that might have been played by Garth Hudson of The Band.