Another user recently ran into this.
The parasite drag tool has a bug if you use a propeller in the Set. This bug will be fixed in the next version, but for now the best thing to do is not include the prop.
Even when the bug is fixed, it won't make sense to include a propeller in the parasite drag tool.
The parasite drag tool does a simple drag buildup -- all the parts are not moving, their wetted area and thickness (or fineness) are used to calculate a form factor. All components are assumed to have attached flow, etc.
A propeller is typically not book-kept as drag -- instead, it appears as thrust.
Assuming your propeller is mounted in front of a wing, there are two sources of increased drag that you need to worry about.
1) In the prop-wash, the wing experiences super-velocities that will increase the local dynamic pressure, increasing the force due to the local skin friction coefficient. You might also assume earlier transition to turbulent flow (or fully turbulent flow). To model this in OpenVSP's parasite drag tool, you would need to come up with an interference factor your self and put it in. You might be able to use subsurfaces to chop the wing into segments that are blanked or not blanked, but that will also be pretty manual.
If you are using VSPAERO's parasite drag estimate for the wing, it may actually do a reasonable job of capturing this without a lot of muss and fuss.
2) Between the increased dynamic pressure and the swirl changing the local angle of attack, you will get a very lumpy lift distribution. This will result in an increase in induced drag. VSPAERO should be able to capture this if you model the propellers power-on.
Neither of these are going to be easy or simple calculations. I recommend you take your time, start with more simple cases, and work to build your expertise with these tools before taking on something of this complexity.
Rob