Using the Positive model allows you to subtract it from other solids, making a recess for the battery. In this config, the bottom of the recess is square to allow battery insertion, and the LED should stick out the top.You could fiddle with it to allow the LED to be embedded into the print, but you'd want to remove the dome, and reverse the square part of the recess.The parameter center_height is the height of the center of the battery. The recess also extends 2mm below the deck to make sure the surface it is being subtracted from gets removed.Octo-led is an example of removing the throwie from an existing model, in this case the classic http://www.thingiverse.com/thing:8896