Glycerol in main buffer

Listen, is it true that glycerol (at 3% v/v concentration) in main buffer (and in samples of analyte) may make the experiment useless as there would not be any signals from eg protein-sugar interactions?

There are papers where 6.5% (w/v) glycerol is added to the running buffer (main buffer?) and the sensorgrams do still lock beautiful so that should not be a problem. In this case small molecules (500Da) are measured with "drug-like properties" (aromatic ring systems) that do have a higher impact on the refractive index = signal than e.g. sugar moieties.
Just dilute your analyte stock 1000-fold in running buffer to eliminate any buffer differences between stock and running buffer that could lead to large bulk effects which overlay your signal.

Strada