Without this extension there is only one "level". This extension uses the layers functionality from the Enhanced Images extension. Published modules don't know about this and so the pins are on the bottom layer. As the GM, just switch to that layer to access your pins (links) - use the "Toggle between the top and bottom layer" button in the image toolbar.
See the first 2 posts here for more info on how to use the layers, and the gotchas:
https://www.fantasygrounds.com/forum...n-CoreRPG%2529
If the extension is running correctly it should put the NPC tokens from the encounter on the top layer (play layers) when you deploy the encounter to the combat tracker. I've just tested this and it's working correctly - clicking the down arrow at the bottom of the encounter window deploys the monsters to the combat tracker and, if they have pre-placement, the tokens to the top (play) layers. How are you deploying the encounter?