We analyze a Josephson junction between two superconductors interconnected through a normal-state nanostructure made of two parallel nanowires with embedded quantum dots. We study the influence of interference effects due to the Aharonov-Bohm (AB) and Aharonov-Casher (AC) phases for local and nonlocal (split) Cooper pairs. In the AB effect the phase of electron is affected by magnetic flux, while in the AC effect the phase of the electron in solid state can be modified due to the Rashba spin-orbit coupling. In the low-transmission regime the AB and AC effects can be related to only local or nonlocal Cooper pair transport, respectively. We demonstrate that by the addition of the quantum dots the Cooper pair splitting can be made perfectly efficient, and that the AC phase is different for non-spin-flip and spin-flip transport processes.