>>It's too late now, but how do you educate your ear?<<
1) tune up one string with your electronic tuner 2) tune the others to it by whatever method you prefer* 3) check them against the electronic tuner and see how close you got.
Do this every time you practice, and your ear will become educated.
*Many different ways of doing this have been recommended over the years. All have their own plusses and minusses, but this one works well for me, so you might like to try it.
1)Tune the 6th (low E string)with the e-tuner. (Like some prevous posters, I find this easier to do using the octave harmonic at the 12th fret rather than the open string.)
2) Match the 7th fret note on the 5th string to the 12th fret harmonic on the 6th string.
3)Match the 2nd fret note on the 4th string with the 12th fret harmonic on the 6th.
4)Match the open 1st string with the (double octave)5th fret harmonic on the 6th.
5)Match the 5th fret note on the 2nd string with the (double octave)5th fret harmonic on the 6th.
6)Match the 9th fret note on the 3rd string with the (double octave)5th fret harmonic on the 6th.
One advantage of this method may be that all those notes are "E" (albeit in different octaves)so your ear(or brain) gets used to that sound. Or it may be that using just one string to check all the others produces a more consistent result than going from string to string across the neck, as many of us were taught to do originally. anyhow, I find this one works better than any other method I've tried so far.