I used pine to make the neck. This is not the normal wood for guitar necks, but it is cheap and you make need to have a few gos before you get it right. The piece was around 28mm thick, 106 mm wide and 738 mm long. The two sides you will be machining should be as parallel as possible.
Fix the neck blank to the spoil board - with clamps or double-sided tape whatever works for you - make sure the toolpath doesn't collide with your clamps. The blank should be aligned centrally with the spoil-board.
I drilled 6mm indexing holes at either end of the neck blank, in the centre line approximately 10mm from either end. It is important that the exact location corresponds to your spoilboard indexing holes and should be outside the finishing and roughing toolpaths so you don't cut through the dowels.
Once you have drilled the first two holes, flip the neck over put in the dowels flip the neck over and drill two more. You could simply drill straight through in one go if your machine is well aligned.
You should use wooden dowels or something that will not damage your endmill if you machine though the dowel by accident.