If you want to configure SharePoint via code you can use the methods available in the Microsoft.SharePoint.Administration namespace.

For example, to configure the Usage Logs:

                SPUsageSettings usageSettings = SPWebService.AdministrationService.UsageSettings;

                usageSettings.LoggingEnabled = true;
                usageSettings.NumberLogFiles = 5;
                usageSettings.LogFilesDirectory = "c:\\logs";
                usageSettings.UsageProcessingEnabled = true;

                usageSettings.SetProcessingInterval(1, 0, 1, 0);

                usageSettings.Update(false);