Beam breakup instability is a potential issue for all particle accelerators and is often the limiting factor for the maximum beam current that can be achieved. This is particularly relevant for Energy Recovery Linacs with multiple passes where a relatively small amount of charge can result in a large beam current. Recent studies have shown that the choice of filling pattern and recirculation scheme for a multi-pass energy recovery linac can drastically affect the interactions between the beam and RF system. In this paper, we further explore this topic to study how filling patterns affect the beam breakup instability and how this can allow us to optimise the design in order to minimise this effect. We present a theoretical model of the beam-RF interaction as well as numerical modeling and show that the threshold current can vary by factors of 5, and potentially, even more, depending on the machine design parameters. Therefore a judicious choice of filling pattern can greatly increase the onset of BBU, expanding the utility of future ERLs.