Patch, I agree that you do need to play a bunch of 12 strings - they can be more different than sixers and a lot depends on how you plan to play them. Just for comparison here are my three - D12-28, home made OM and long scale ladder braced copy of a Stella.
I think the best commercial twelves on the market are made by Taylor and Guild - be sure to play some of them. Breedlove is doing some interesting work and the Martin Grand jumbos are probable their best modern 12's. When you play them remember that many 12 string players like to down tune one or two semi tones - if you want to tune to concert short scale and light strings are a good idea.
To try to describe how I lay out the string spacing - first remember that normally the first two courses are unisons tuned the same as a six string. The next four "courses" normally have the primary string "down" (closer to the floor) and the octave "up" - you hit it first with your pick. There are other ways to string but lets not get into them here.
I lay out the two outside strings whatever distance I like from the edge of the fretboard - that depends on playing technique, do you fret with your thumb, bend notes, etc - but lets just say its 0.110 from the edge. That will be the high E and the low octave E. Next make a mark on the nut 0.100 inside the low E octave - that will be the low E primary. Now space the four additional primaries using your usual approach - for me its the SM scale. Now make a mark 0.100 to the left of each of these - that will be the octaves. Look at it, fiddle with it slightly until it looks right, cut the notches.
This is a crappy picture but you get the idea maybe
I play a lot of slide on my twelves so I do two additional steps. First I like flatter than normal fretboards - I use 20 inch radius rather than 16. Second, I cut the nut slots so that the tops of the strings are roughly level rather than the bottoms. For normal fretting you want the bottoms of the strings to approach the zero fret line.
As Tim points out, spacing at the saddle is set by pin locations but can be controlled a little bit by ramping. On the Stella clone I used a tailpiece so spacing is set by slots in the saddle. Note in Tim's picture that he has compensated each string of each course - that is a lot of work but it sure helps the guitar play in tune up the neck - 12 strings are notorious for poor intonation.
Definitely need to give that a try sometime. I'll probably keep to 1" or less difference though. But at least the wide neck helps reduce the angle on the frets.