The Automated Planet Finder (APF) was originally designed as a single purpose facility to search for exoplanets. The APF, however, has become a general use observatory that is used by astronomers the world over. We describe the improvements to our software for operations that both optimize finding planets with known periods and supporting a much broader community of astronomers with a variety of interests and requirements. These include a variety of observing modes beyond the originally envisioned fixed target lists, such as time dependent priorities to meet the needs of rapid varying targets, and improved tools for simulating observing cadence for the planet hunting teams. We discuss the underlying software for the APF, illustrating why its simplicity of use allows users to write software that focuses on scientific productivity. Because of this simplicity, we can then develop scheduling software, which is easily integrated into the APF operations suite. We test these new scheduling modes using a nightly simulator which uses historical weather and seeing data. After discussing this new simulation tool, we measure how well the methods work after a 36 month simulated campaign to follow-up transiting targets. We find that the data yield of each of the tested schemes is similar. Therefore, we can focus on the best potential scientific return with little concern about the impact on the number or duration of observations.