Separation of variables in quasi-potential systems of bi-cofactor form

We perform variable separation in the quasi-potential systems of equations of the form $\ddot{q}=-A^{-1}\nabla k=-\tilde{A}^{-1}\nabla\tilde{k}${}, where $A$ and $\tilde{A}$ are Killing tensors, by embedding these systems into a bi-Hamiltonian chain and by calculating the corresponding Darboux-Nijenhuis coordinates on the symplectic leaves of one of the Hamiltonian structures of the system. We also present examples of the corresponding separation coordinates in two and three dimensions.