just start with the sugguestions in the manuals and then modify them and experiment. thats the best part of modular gear is you can make it your own sound
It sounds like what you need is also the Vx352. THat way you will have the CV Inputs AND Outputs of the RME. That way you could use the RME to control the Foogers/Phatty parameters, or with the 352 you could use the foogers to modulate the parameters of the RME.
It seems to me that you can definately get duophonic voicings with the phatty and the RME and depending on what Foogers you have will depend on the tricks up your sleeve.