I don't know why everyone else tunes from the low E. I find it a lot more convenient to start by tuning the D string (third lowest sounding) to whatever will give me a concert pitch note that is doesn't waver (you don't want to try to tune to an accordion, for example). If there's one in the room, I use the piano setting on an electronic keyboard. Then tune the strings above D, by fretting at the fifth fret on the D string, fourth fret on the G string, and fifth fret on the B string. In each case, you adjust the next highest string so it is playing the exact same note as the fifth or fourth fret of the string below. If it is close but not quite the same, you will hear a wavering sound as you pluck the two strings simultaneously. When they are at the same pitch you just hear a solid tone.
Then tune the two bass strings below the D. The easiest way is to finger the second fret on the D string, so you are playing an E, and tune the bottom E string to that note, 1 octave lower of course. Again, the beating sound will tell you if the two strings are in tune with each other. When the low E is in, tune the low A (second lowest string) to the fifth fret of the low E string.
It really is better to tune a guitar to itself than to tune every note separately to an electronic tuner. Faster too. You should have a good tuner, but that doesn't mean you should use it to tune every string you ever touch.