Squeak and rattle are annoying sounds that are often regarded as the failure indicators by car users. Geometric variation is a key contributor to the generation of squeak and rattle sounds. Optimisation of the connection configuration in assemblies can be a provision to minimise this risk. However, the optimisation process for large assemblies can be computationally expensive. The focus of this work is to propose a two-stage evolutionary optimisation scheme to find the fittest connection configurations that minimise the risk for squeak and rattle. This was done by defining the objective functions as the measured variation and deviation in the rattle direction and the squeak plane. In the first stage, the location of the fasteners primarily contributing to the rattle direction measures are identified. In the second stage, fasteners primarily contributing to the squeak plane measures are added to the fittest configuration from phase one. It was assumed that the fasteners from the squeak group plane have a lower-order effect on the rattle direction measures, compared to the fasteners from the rattle direction group. This assumption was falsified for a set of simplified geometries. Also, a new uniform space filler algorithm was introduced to efficiently generate an inclusive and feasible starting population for the optimisation process by incorporating the problem constraints in the algorithm. For two industrial cases, it was shown that by using the proposed two-stage optimisation scheme the variation and deviation measures in critical interfaces for squeak and rattle improved compared to the baseline results.