PatchWork 1.7 introduced the ability to route auxiliary outputs from virtual instruments straight into your DAW. Our friends at Pro Tools Experts have written a tutorial that shows you how to do the routing easily inside Pro Tools, check it out!
Note: this tutorial uses BFD ECO as an example, but it applies to any instrument that provides auxiliary outputs.
Tutorial: Routing BFD ECO auxiliary outputs from PatchWork to Pro Tools
Enjoy!