If you're going to use measured weight to measure CG, the measuring points are arbitrary. You simply need to fix the position of your measuring points, pick one as your reference point (or an unweighed point that you know it's position relative to the others), and the CG you calculate will be relative to the reference point. At that point it's no more complicated than measuring the CG on a trailer.
There are better and worse points to work form than others -- pick points too close to the CG and you'll find your calculation becomes sensitive to measurement error. For instance -- one on the nose, and two in the wings about half-way back on the chord are probably not great spots. Ideally the CG will be near 1/3 of the chord, so the wing CG points will weigh a lot but have very short measurements, and the nose may weigh very little but have a long measurement. Fundamentally, the smaller the measurement, the more impact any error will have. Picking the points more spaced out (say, one in the nose, and one on each tail surface) will more evenly distribute the weight among the supporting points (making weight measurement errors equal at all points) and make length measurements easier (reducing the errors in the length).
. . . all that being said . . .
two fingers -- one under each wing -- can be a VERY effective CG estimator. I appreciate the desire for the precision, but for something that light and small, anything more is probably overkill.
Calculate the ideal CG (there are several calculators online), mark on the wing, measure with your fingers and move the ballast until it's just slightly forward of those marks (or leans nose-down when your fingers are on the ideal marks) . . . then fly.
This thing used to be a chuck glider -- it should still glide. Load her out for flight, get the CG about right, and run a few glide tests over tall grass (leave the prop off until maiden -- the missing weight is negligible but they can break easily in test landings). So long as the control surfaces are functioning in the right directions, you should be happy with the results
