They are separate. They do not have anything to do with one another.
They are different tools. VSPAERO only knows about the components participating in the VSPAERO model. The Parasite Drag tool can make all kinds of adjustments to different components and can include things not in the VSPAERO model.
The VSPAERO model does a strip-wise model on lifting surfaces that knows about the local velocity, Reynolds and Mach numbers. This is particularly a benefit for rotating wings.
There are changes underway to the VSPAERO parasite drag model that will be a big improvement.
The tools will still most likely stay separate.
Rob