Properly tune as in? The tuning of a 12-string is
ee-bb-Gg-Dd-Aa-Ee
where the highest two pairs of strings are of the same octave, and the other pairs have the lighter string an octave higher than the complement strings, which are tuned like a normal guitar.
I'd trust a tuner more than I would my own listening, but that's just me. Hope that helped.