Using the example of two closely spaced localized alkaline-earth atoms, we consider the possibilities of the quantum beat method (a version of the level-crossing spectroscopy in a magnetic field) in finding two parameters characterizing the system, namely, the direction from one atom to another and the distance between them. The applicability of the method to the nanoscopy of systems of closely spaced quantum dots, vacancy centers (NV centers, etc.), and impurity atoms (molecules) in crystals is discussed.