Just squint at it and pick something reasonable. It won't make a very big difference.
There is no such thing as a NACA 2010 -- the 2nd digit is the location of maximum camber, which can't be at the LE.
Comparing the 0010, 2410 and 2210, their ideal lift coefficients are 0.0, 0.256 and 0.308 -- which are faithfully pretty much at the center of the drag polars for those airfoils.

If instead, you compare a 0010, 2410, and 4410 (same camber position, but increasing magnitude), you get ideal lift coefficients of 0.0, 0.256, 0.512
Of course, these charts are just at one Reynolds number.
What VSPAERO is doing is applying a very simple drag model strip-wise along the wing. It calculates the local cl and then adds in a simple polar term that basically amounts to:
cd = cd0+K*(cl-cl0)^2
So, by adjusting cl0, you are just moving where the center of that polar is. It is a very simple approximation.
Since the coefficient ends up multiplied by area (first by chord, then by span), I would say an area-weighted average is best.
Rob