No magic to it -- draw a line between the balance points at the tips and where it intersects the wing saddle is the balance point at the root (obviously). The manufacturer might give a measurement for the CG at the root or the tip, so it's easiest to measure the same way the manufacturer does. If you really wanted you could measure the sweep of the leading edge and do it otherwise.
If you're not using the manufacturer's measurements, you can probably choose any way you like and stick to it; it only matters where the CG is relative to where you've had it previously.
On some designs you do need to be careful about how you do it. For example on a glider with a light body and lots of dihedral in the wing, it'll never seem to balance if you do it at the root because most of the plane's weight is *above* the balance point, so it's unstable. If you do it at the tips, the weight will be so far *below* the balance point that the plane may seem to balance level more or less anywhere along the chord! On such a design, you'd need to balance somehere in the middle of the span.
Generally, you balance high wings upright and low wings inverted, because otherwise the weight above your balancer makes the system unstable, so it never seems to balance.
There's a way to sidestep all of this, which is to hang the plane from the ceiling with light string and hang a plumb bob (spelling?) from the same point. The bob always points through the (3 dimensional) CG, so get the plane level and it'll point to the right place no matter what. Takes forever to get the plane to quit swinging though