I believe the way that the flat mould maker gets the reverse onto the plaster is to transfer the original drawing onto tracing paper.
They simply make a tracing of the two faces back and front transfer the front onto the appropriate block and the transfer the rear to the correct face on the other block.
You must be able to line up both tracings so that each is exactly centralised so that the two drawings lie in the correct position when onto top of each other to make your match.
I would suggest that you place a number of pencil lines on both blocks. one down the enact centre one across the middle, then one from each corner, that should establish the exact centre of each block, you have to check your measurements to make sure that each entre is in the same place. Centralise tour tracing, transpose the tracing onto the block, same for the reverse and again check that all lines up. Then cut you mould.
You will also need some soft plasticine which you can press into the pattern as you cut to constantly check that you are cutting correctly.
Good luck.
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The simplest way would to make a master front and back then pour your plaster over that, but again you will have to centre the pattern, I suppose that having made one master this way, you could simply higher the side of your mould box and pour the back straight onto the front. You will have to have some release agent between the two halves, otherwise they will never part?
Hope this helps.
Kind regards
Bob