You educate your ear through practice. I'm not keen on the use of electronic tuners, except in noisy situations, because they make your ear lazy. You should be able to tell whether your instrument is in tune, identify where it's out and put it right.

Tuning using harmonics can help because it is a purer tone, especially if you're using a tuning fork which makes a very similar tone.

If you can't tell whether two notes are the same listen for the "beats". These are caused by the sound waves at slightly different frequencies interfering with each other. When you've eliminated the beats, they're in tune.

I must admit I do use an electronic tuner but only for hammered dulcimer - with more than 100 strings to tune I think I have an excuse. I still rely on my ears for the final adjustments.