We consider a system of three weakly coupled Bose-Einstein condensates and two atomic quantum dots embedded in the barriers between the condensates. Each dot is coupled to two neighboring condensates by optical transitions and can be described as a two-state system, or a pseudospin 1/2. Although there is no direct coupling between the dots, an effective interaction between the pseudospins is induced due to their coupling to the condensate reservoirs. We investigate this effective interaction, depending on the strengths of the dot-condensate coupling T and the direct coupling J between the condensates. In particular, we show that an initially ferromagnetic arrangement of the two pseudospins stays intact even for large T/J. However, antiferromagnetically aligned spins undergo peculiar “breathing” modes for weak coupling T/J < 1, while for strong coupling the behaviour of the spins becomes uncorrelated.