At some point there will be PCB package template files for a board to plug in the Samtec expansion connector, but until someone gets round to doing that, here is the collected wisdom. Thanks to Glen VanMilligan for pointing out most of them.
The segments of the connector are labelled numbered A-E, with A being at the left hand end (with the connector facing you and at the bottom of the board) - see: http://www.balloonboard.org/hardware/205/con/samtek.html
Note that on the central segment (C1-40) the 4 'extra' pins are tied to 3V VCC, whilst they are ground on the other 4 segments.
The schematic calls the first segment (pins A1-A40) 'J140B', and the next segment (pins B1-B40) 'J140C', in a slightly confusing manner. Just be aware.