To find eigenvectors for two matrices A and B using the generalized Jacobi method, one must consider the simultaneous diagonalization of the matrices. While eigenvectors are specific to each matrix, simultaneous diagonalization is relevant when the matrices commute, as shown in quantum mechanics with operators X and Y. The discussion highlights that if KM does not equal MK, the matrices cannot be simultaneously diagonalized, complicating the eigenvector determination. An example is provided with matrices K and M, illustrating the conditions under which diagonalization is possible. Ultimately, the conversation emphasizes the importance of matrix commutation in the diagonalization process.