The Tuner should be used as visual feedback to train the ears.

Once the ears can hear the beats, the tuner is superflous, you'll find that you not only no longer need it, you can even reach up and adjust a string that goes out as needed, while playing.

The human ear and the gray matter that is connected to it is an amazing test instrument in and of itself. One can even get to the point where they can perform intonation adjustments at the bridge using nothing other than the ear - and be "spot on" every time.

I realize that such is not for everybody, those who are inclined should investigate it, though. Training the ear to know exact intonation not only comes in handy for tuning the instrument, such can make a world of difference in Performance as well. Each note of the Tempered Scale soon becomes familiar like an old friend.

Those who have been using tuners of ANY type, stroboscopic or digital, may be surprised by how well that visual feedback has already trained their hearing, BTW. I've had students put the tuner away for awhile and most of them find out what they can really hear when tuning their guitars only then.

With the guitar, one can also feel the Beats between two notes that are supposed to be the same note, but are a few cycles "off" of each other, in the back of the neck as modulated pulsing. Feel it, then work towards hearing it.

In the Physicist's world, the science of matching two frequencies exactly is called, "Zero Beating" for a reason.

--Mac