The Tuner typically works best if it's used before any other effects (like the Guitar Amp).
The A box determines the frequency of note A5. The Tuner effect can be used to measure the frequency of an A5 played on, for example, a piano. This value can be entered in the A box, so other instruments can be tuned to the same pitch.
Note: in order to use the Tuner effect you should engage the track's Rec button. Alternatively you can make sure Practice Mode is being used.