When using autoloading, sampa will resolve addresses like localhost/MyModule/MyAction to App\MyAppname\MyModuleController and call MyModuleController->MyAction, so you have to add the prefix "App" to your autoloading routine (see dist/index.php.dist). The same approach is required for Workers, when running a worker, sampa will resolve parameters like MyNamespace\MyWorker to Worker\MyNamespace\MyWorker (see dist/boss.php.dist).
During Kernel/Boss boot, you can setup the path to your *.config.php files and the path to log files, by using the first and second parameters respectively (see dist/index.php.dist and dist/boss.php.dist).