I'm not 100% sure I understand you - but if I do, then I think yo'd want to look into Unity's limitations, and how things (mostly) needs to be inside of the Assets folder.
As I understand you, this is not a PlayMaker related question, but a general Unity question.
Anyway, IF you have a folder that is acessible by Unity in Playtime, then surely, it's not a problem to have PlayMaker handle the rest..
I hope this helps you a little further