Ed's question is a good one. He is getting some answers to another good question, but one he didn't ask.
To answer the one he didn't ask, most acoustic 12 strings have the octaves in the even numbered positions counting from the highest E. That means the first string you hit on a down stroke is the octave. Rickenbacker electrics have them reversed - that probably gives Ricks their characteristic sound. I know people do experiment with Rick tuning but most settle on the "normal" Taylor/Guild/Martin ordering of the strings in each course.
The question that I think he was asking is which row of pin holes do you put closest to the saddle. On a Guild it is the primaries, on Taylors and Martins it is the octaves (with the exception of the Martin Grand J which for some reason seems to be reversed).
I own a D12-28 and made an OM sized 12 with the octaves closest to the saddle I also built a ladder braced 12 with a tail piece, obviously that doesn't count. I think there are two minor factors in this decision - it seems like the string closer to the saddle has the sharper break angle - closer to 45 degrees while the farther one has a pretty shallow angle. Whatever your thoughts about the effect of break angle might influence this.
Second, by putting the octave farther away you can get it just a hair closer to the primary (its smaller diameter would let it sneak by the pin of the primary). Most 12 string players want the courses as close as possible but there are a few like Chris Proctor who space them wider and can pick individual strings.
There is also the two strings to a pin design - I think it would be a hassle to change strings but you do see it from time to time.
I used a premade Martin bridge on mine but if I was going to do it again I would probably reverse them and put the primaries closest to the saddle
