I don't know how 3wfab does his, but on mine, you draw a nice 2d drawing in CAD. I use AutoCAD at work, so I've got good access, and 2d drafting like this is pretty quick and easy. I draw the frame out as it would sit in the bike, and then you have an offset concentrically from the bottom bracket. For mine, you basically draw a line from the center of the BB to an extension line from the head tube (perpendicular). Offset that by 3" below the centerline of the BB. From there, it's really just basic geometry to get all the lengths of tubes you need.
To do the rear triangle, you extend your "offset" line backwards past the dropouts. Draw a line from the center of the dropout perpendicular to the offset line. That tells you how far back along the fixture spine to set your dropout mount, and how far up from the spine you need to set your dummy axle holder.
It's all actually pretty slick and pretty simple to use. It's based off of a fixture that James at Black Sheep built for Rob Pennell (Badger) several years ago. Another friend has that fixture now, and I just want to build my own to a)not have to borrow his for 2 weeks at a time and b)make a few minor improvements to have more room to get the torch into places (especially under the BB).