In the board.
Mirroring (or selection of which side of the board) is a geometric consideration. It's purely related to physical construction and not functionality. It's merely an aspect of component placement, which is why it's also available from the middle mouse button during a "MOVE" operation. All these things should tell you that you do it in the board editor, not the schematic.
The mirror command is available in the schematic editor but its function there is to allow you to show gates (or op-amps, transistors, etc.) flowing right-to-left instead of left-to-right. That has not bearing on the physical layout of the board any more than moving your resistors symbols into a line on the schematic would.
