The BSP-100 beam position monitor (BPM) was commissioned and installed at the Advanced Photon Source (APS) in a fraction of the ring as an upgrade to the present turn-by-turn BPMs. Keeping the same rf front end of the present BPMs, the BSP-100 BPM adds a high-speed analog-to-digital converter and uses a field-programmable gate array (FPGA) to perform the signal processing. The main advantage of the new system is a much better signal-to-noise ratio as all the bunches in the stored beam can now be (selectively) sampled each turn. The implementation requires a much more complex timing control. We report on the high-level software that controls, saves, restores, and compares the timing of the BSP-100 BPM. This software uses Tcl/Tk for the graphical user interface, the SDDS toolkit for data processing, and SDDS-EPICS compliant tools for saving and restoring.