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Double-well systems loaded with one, two, or many quantum particles give rise to intriguing dynamics, ranging from Josephson oscillation to self-trapping. This work presents theoretical and experimental results for two distinct double-well systems, both created using dilute rubidium Bose-Einstein condensates with particular emphasis placed on the role of interaction in the systems. The first is realized by creating an effective two-level system through Raman coupling of hyperfine states. The second is an effective two-level system in momentum space generated through the coupling by an optical lattice. Even though the non-interacting systems can, for a wide parameter range, be described by the same model Hamiltonian, the dynamics for these two realizations differ in the presence of interactions. The difference is attributed to scattering diagrams that contribute in the lattice coupled system but vanish in the Raman coupled system. The internal dynamics of the Bose-Einstein condensates for both coupling scenarios is probed through a Ramsey-type interference pulse sequence, which constitutes a key building block of atom interferometers. These results have important implications in a variety of contexts including lattice calibration experiments and momentum space lattices used for quantum analog simulations.