Tuning a 12-string is a bit o' black magic, but it's very satisfying when you get is sussed.

Tune the main strings first. You have to mute the thinner octave strings to avoid confusing the tuner. Then tune the octave strings, starting with the high E and the B strings. The second high E and the B strings are tuned to almost the same pitch as the main strings. They should actually be very slightly higher than their main strings. When you play both strings at once, there should be a slow warble to the sound as the two slightly different frequencies 'beat' against each other. Continue working your way to the lower pitched strings, tuning the thinner octave strings very slightly higher than the thicker main strings. I mean a full octave above, plus just a little bit.

When you're done, a stroked chord should ring, with just a bit of warble to it, making it sound very full compared to a 6-string. When you get it just right, it's like a combined octave/chorus effect.