IE3D has a "circuit simulator" also (I don't have experience with it) where you want the capacitor, you need to add a port and that port appears in modua where you can add lumped components.
Why not adding the capacitor in the geometry? When you have two flat plates, facing eachother exactly, close together, you can use the approximation formula:
C = eps.0*A/s (A = surface area of one plate, s = distance between plates). The actual capacitance is somewhat more then based on the formula.
Check that the meshing of each capacitor plate is exactly the same, so the meshed surfaces should face eachother exactly.
You can "tune" the capacitor by changing the distance between the plates, or the size.