I've been using this, it's super helpful. The workflow I've found is to develop patches inside Pd-Extended using this Mother Patch. I try to use only vanilla objects but I'm not 100% percent what's vanilla and what's not (I'm coming from Max/MSP).
Once I have the patch working, I open it up in Pd-Vanilla and check for errors creating objects. For each object that throws an error, I copy the individual compiled externals from here: http://forum.critterandguitari.com/t/pd-extended-objects-for-organelle/183 into the same directory as the patch. Pd-Vanilla on my Mac still throws an error because (I think) those externals are compiled for Arm, but when I open on the organelle everything works.
I'm super happy with having this little dedicated box for Pd. I think the "remote" workflow could use some streamlining. For beginner users just entering into the Pd world, I'd definitely recommend developing right on the organelle using an external monitor, keyboard, and mouse. Super great start though! I'm very inspired by this little machine.