In a recent work, Murmann et. al. [Phys. Rev. Lett. 114, 080402 (2015)] have experimentally prepared and manipulated a double-well optical potential containing a pair of Fermi atoms as a possible building block of Hubbard model. Here, we carry out a detailed theoretical study on the properties of both fermionic and bosonic two-site Hubbard models with a pair of interacting atoms in a trap with a double-well structure along z-axis and a 2D harmonic confinement along the transverse directions. We consider fermions as of two-component type and bosons as of spinless as well as of two spin components. We first discuss building up the Hubbard models using the model finite-range interaction potentials of Jost and Kohn. In general, a finite range of interaction leads to on-site, inter-site, exchange and partial-exchange terms. We show that, given the same input parameters for both bosonic and fermionic two-site Hubbard models, many of the statistical properties such as the single-and double-occupancy of a site, and the probabilities for the single-particle and pair tunneling are similar in both fermionic and bosonic cases. But, quantum entanglement and quantum fluctuations are found to be markedly different for the two cases. We discuss atom-atom entanglement in two spatial modes corresponding to the two sites of the double-well. Our results show that the entanglement of a pair of spin-half fermions is always greater than that of spinless bosons; and when the fermions are maximally entangled the fluctuation in the two-mode phase difference is largely squeezed. In contrast, spinless bosons never exhibit phase squeezing, but shows squeezing in two-mode population imbalance depending on the system parameters.