An old conjecture claims that commuting Hamiltonians of the double-elliptic integrable system are constructed from the theta-functions associated with Riemann surfaces from the Seiberg-Witten family, with moduli treated as dynamical variables and the Seiberg-Witten differential providing the pre-symplectic structure. We describe a number of theta-constant equations needed to prove this conjecture for the N-particle system. These equations provide an alternative method to derive the Seiberg-Witten prepotential and we illustrate this by calculating the perturbative contribution. We provide evidence that the solutions to the commutativity equations are exhausted by the double-elliptic system and its degenerations (Calogero and Ruijsenaars systems). Further, the theta-function identities that lie behind the Poisson commutativity of the three-particle Hamiltonians are proven.