Coarse-grained FPGA overlays improve design productivity through software-like programmability and fast compilation. However, the effectiveness of overlays as accelerators is dependent on suitable interface and programming integration into a typically processor-based computing system, an aspect which has often been neglected in evaluations of overlays. We explore the integration of a time-multiplexed FPGA overlay over a server-class PCI Express interface. We show how this integration can be optimised to maximise performance, and evaluate the area overhead. We also propose a user-friendly programming model for such an overlay accelerator system.