Coming back to this:
To Rob's point, by matching the local Cl you are matching the operating condition of the airfoil and therefore the wing. You are effectively saying that for a wing producing some amount of lift, inviscid or not, use XFOIL to predict the drag contributions from pressure or form drag. The friction drag is relatively independent of angle of attack and will be mostly dependent on freestream speed. VSPAERO makes an attempt at correcting for the non-linearity of the viscous component by fitting CD0 with a NACA 0012 empirical model. Circling back around, you've said that you are trying to accurately account for the profile drag of each section but haven't really stated "why". Are you using VSPAERO to compute the induced drag and supplement this value with XFOIL's viscous component? To what end? What is the end goal of your work? Why do you need an alpha-based method vs a lift-based approach? Or, instead, are you evaluating a wing design to capture spanloading and trying to use XFOIL to capture the drag...? In which case we get back to using Cl to predict Cd(total) and then integrate over the span.
Also, since you are using XFOIL I wanted to get a clarification. From the XFOIL documentation below, CD is the total drag, CDf is the skin friction drag (form drag, profile drag), and CDp is the pressure drag. Which of these values are you trying to isolate? I'm assuming the viscous friction/form drag is what you are after.
In addition to calculating the total viscous CD from the wake
momentum thickness, XFOIL also determines the friction and pressure
drag components CDf,CDp of this total CD. These are calculated by
/ _
CDf = | Cf dx CDp = CD - CDf
/
Here, Cf is the skin friction coefficient defined with the
freestream dynamic pressure, not the BL edge dynamic pressure
commonly used in BL theory. Note that CDp is deduced from
CD and CDf instead of being calculated via surface pressure
integration. This conventional definition
/ _
CDp = | Cp dy
/
is NOT used, since it is typically swamped by numerical noise.