Creating a slotted & plated through-hole in EAGLE: where to draw milling outline
I recommend drawing the slot in the footprint. Perhaps creating two versions of the part.
With and without (only larger hole).  Since plated slots are a paid extra with most PCB manufacturers that might not be necessary for some prototypes.

To do this, draw the slot on the dimension (20) or milling (46). Which does not matter, unless your fab house explicitly asks for plated slots to be a separate layer.
Dimension will be guaranteed to be outputted to Gerber and sent to the fab house, milling is not.  

To make a slot plated, simply put copper right to or over the slot on both layers.

The slot is probably not visible on your board since either you didn't update the library in the project, or layer Milling (46) is not visible.

In eagle, it will never show as slot pads layer, contrary to other packages that natively support a plated slot pin. 

An example is the POWER_JACK_SLOT and POWER_JACK_PTH in Sparkfun_Connectors.



The difference between the two variants in the Sparkfun library is the milling layer within in the green pad. Pads layer (17) is also copper, except on all layers. This means the slot is already surrounded with Pads layer, thus copper.
The crosshair is the drill mark on Holes (45) or Drills (44) layer, that is visible on any drill hole.
(if those layers are active)