Close, 1 goes to 2, 2 goes to 1
1 - 2
2 - 1
3 - 4
4 - 3
5 - 6
6 - 5
and so one...
When I make my cables, I use a razor blade to split every two lines of the ribbon cable making 22 pairs. Then I twist each pair once so that each pair is reversed (I use tape to hold each reversed pair in line as I twist the next pair and leave about an inch over lapping). Then I press the ribbon cable end on, The other end just has a normal end with no line reversed or any thing.
This method takes time and practice, the much easier method is to not split the ends but to put two connecters next to each other and install the cable on the middle of the four ends, here's a picture from BadFlash http://www.badflash.com/images/double.jpg This method is a lot easier and requires just a extra third header.