When you run the View -> 3D Model command, in APD you must manually configure the die thicknesses and relative heights. On the 3D Layer Stackup tab, RMB on the layer number (e.g. "1") on the left side of the grid and select the Add option. When you set the type to "DIE", you'll be able to select the die refdes from the list in the name column and specify the pad height and the component thickness.
To leave a space between items in a stac, and a "SPACER" entry. Or, if you have multiple different die stacks and need to move back down to start adding entries in a different stack, add a spacer with a negative thickness before adding the next die.
Note: If you have SiP Layout instead of APD, all of this information is configured automatically for you from the information you specify in the die stack editor. APD is not intended for use as a stacked die substrate design tool. SiP is.