The Tune User Interface is divided into three main sections. One section allows you to autotune the instrument. A second section lets you manually tune various parameters on the instrument. The third section is a toolbar which is visible with both of the other sections.
You can only use Manual Tune if your instrument is an LC/MSD or LC/MSD XT.
Tune > Autotune/Checktune Section
Tune > Manual Tune Section (LC/MS)