A little clarification: the waterline is not necessarily your "level." Many plans have the vessel flat on it's keel and the stations are drawn at 90° to the keel, which often places the waterline at an angle.
The forms are attached to a building board in some manner that they can be taken loose. For instance, I use plywood forms with wood strips attached that are wider than the forms. The strips, usually 3/4 inch square help hold the form at right angles to the base board, and are screwed down to it. At any time, the screws can be removed and the hull lifted off.
I draw a line 90° to the stations and maybe an inch above the highest point of the hull at the bow or stern. Flip the plan 180° and that's your building base line. Match that line on the body plan and extend each of the stations up to that line. It doesn't need to be a lot - more is a waste of wood.
What's nice is you have a steady point to measure from any where on the model.HMS Macedonian framing completed, just before planking began - the waterline is not level to the keel or the building board. Note also that ALL the forms were removed from the hull when planking was completed.
On getting the lines onto the forms. I used to trace them with tracing paper - place the paper pencil side down on the board and redraw it from the back side - which has a carbon paper effect. Now I make up each one in a drawing program (Paint Shop Pro v7) and print each one to paper and paste that to the wood. I can explain that process in more depth if you require it.