New answers tagged instructions
A rather drastic solution would be to add a 'sticking-up' metal or plastic spike on the purple board just to the left of the connector which sticks up just high enough to prevent the blue board from being fitted across it.
If you happen to have the resources to rearrange your layouts, you could arrange the two rows of plugs and pins in an "L"-or "T"–shape – this way there would only be one way how to plug them.
You don't have a lot of space on your board for markings. I'm going to assume the following: You can't expand the size of the purple board. You can't force a pairing indicator on the blue board (e.g. it's made by some other party). In this case, it's hard to convey precise orientation within these hard constraints. But what you can do with the limited ...
The way you indicate this commonly for atmega chips is to have the half moon symbol printed on the PCB: The convention should be familiar to your target audience, so if you were to put some kind of shape on the board that matched up to a similar shape on the secondary board, then you would have something that would be intuitive. If you don't have control ...
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