How do you tune your software configuration?

There are lots of configurations that one needs to set for a software system. Some affect the performance (e.g., batch size), and some are necessary for correctness (e.g., a reasonable timeout value). How do you set the configuration values in your software products? For instance, what happens if the workload changes and a higher batch size gives a higher throughput? Do you manually change the configurations or use third-party software to set it for you? I believe this is hard to do manually, but I'm unsure if an automatic solution exists to solve it.