To get the stock crystal out, you have to remove the movement, then push the crystal out from inside. Usually it will pop out with just thumb(s).
I just did one a couple nights ago so I could upgrade the insert with a new pearl. Here are some pics.
The crystal just gets pressed back into the already seated gasket. Angle it so one side of the crystal lower step gets inside the gasket, then apply sideways pressure in that direction to help the unseated side overcome the opposite side gasket lip. It usually goes in fairly easily by hand.