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Rotation of X-axis in alignment

I want to keep all features in (+X,-Y ) coordinate in the program because I need to flip the piece and measure some more features at bottom side. So, I want to keep same edge of the piece for X-axis and Y-axis. I would keep X-axis/Lin1 (+X coordinate) at +X-axis and Y-axis/Lin2 (-Y coordinate) at -Y-axis. Do I still have to constraint X-axis at +X rotation in alignment? I thought about -X rotation that would restrict the movement of / by -Y-axis. Please, let me know.