Icons for encounter creatures can be changed, but actual icons will all be the same as original icon.

1) Create an encounter with 5 skeletons by dragging the skeleton record from the M&T module to an encounter record. Make sure that there is a default token for the creature.
2) Notice that there are 5 icons or empty icon "slots" for the monsters. Drag 5 different tokens into the encounter window, 1 for each skeleton.
3) Drag the skeleton icons from the encounter to a battlemap. Each skeleton token will change to a "thumb's up" icon.
4) Close the encounter record.
5) Re-open the encounter record, and click the down-arrow to add the encounter to the combat tracker.

RESULT: The skeleton tokens are all shown on the battlemap, but the custom icons that were used in steps 2-4 are all now replaced with the default token from step 1.

I would *love* for this functionality to work as it look like it should, with the GM able to customize the creature icons. But if that functionality isn't going to be made to work, then I'd suggest just removing the token drag-drop functionality into the encounter window, so there is no confusion.