Using criteria based on superselection rules, we analyze the quantum correlations between the two condensate modes of the Bose-Einstein condensate interferometer of Egorov et al. [Phys. Rev. A 84, 021605 (2011)]. In order to determine the two-mode correlations, we develop a multi-mode theory that describes the dynamics of the condensate atoms and the thermal fraction through the interferometer sequence, in agreement with the experimentally measured fringe visibility. We thus present experimental evidence for two-mode entangled states genuinely involving 40,000 ^{87}Rb atoms, and for two-way steerability between two groups of 20,000 indistinguishable atoms.