My scalar is connected to a generator, and I run programs at night while sleeping. If I also place water and supplements, will the molecular function still work while running frequencies?

The Scalar system can work with both Rife Scalar (frequency programs) and Molecular Scalar (items placed for imprinting). They are not an either/or function.

If you were running frequency programs while placing water and supplements on the boxes, the supplements and water could still receive the molecular imprint. The frequency program running does not prevent the imprinting process from taking place.

The difference is that the frequency programs provide the selected frequency information through the software, while the items placed on the boxes receive the molecular imprint from the objects themselves.

So in your case, you were not only receiving the software frequency programs — the water and supplements could also have received the molecular imprint.