Using quantum transport theory in conjunction with a tight-binding description of the electron interactions with the lattice, we have mapped out the variations in the conductance in single-wall carbon nanotubes when the two vacancies in a well-separated vacancy pair assume all different relative positions. The investigations have been performed for armchair and metallic zigzag carbon nanotubes. It is found that only a very limited number of basically different conductance spectra exist, and that much of the results concerning how the conductance depends on the intervacancy separation can be interpreted in terms of a simple one-dimensional double-barrier scattering model. The total conductance is also analyzed in terms of its constituent eigenchannels to provide additional insight into the conduction mechanism. For instance, eigenchannels can be either totally unperturbed, contain double-barrier scattering resonances, Fano anti-resonances, or be completely blocking in a narrow energy interval, depending on the exact relative positions of the vacancies. Furthermore, and in accordance with experiments, it is found that the region bounded by the two vacancies in a separated vacancy pair can alternatively be regarded as a quantum dot similar to that defined by a semiconductor-metal-semiconductor heterojunction nanotube.