The higher (thinner) strings are usually placed so that the downstroke hits them first. This is the first way you've shown. I think some of the Rickenbacker 12's had it the other way around (like your second example). The slots in the nut will show you which way yours was meant to be strung.

The good Doctor is quite right about the tuning. Tune your 12-string in D (D G C F A D) two steps down from standard E. Put a capo on the second fret to restore the tuning to standard E. The reduced string tension will go a long way toward helping your instrument last longer. And 12-strings don't sound good above the 12th fret anyway, so don't fuss about losing two frets of the neck length. I sold my old Daijon 12-string acoustic this summer. I bought it new in 1977. It still plays as well as it did when I bought it. My Washburn EA20-12B electric acoustic has action comparable to my electric guitars, and it shows no signs of a bowing neck or 'bellying' from having the bridge pull up.