Assemblies are available by opening the Assemblies Panel from the Window Menu or by clicking on in the Mode Toolbar. There is a video that walks through the process of building a module with assemblies. More details are shown in Creating a Model with Assemblies.
Models are constructed using building blocks - stocks, flows and converters - connected together in a meaningful way. Assemblies are self contained models that demonstrate common ways to connect together building blocks and that can be used as parts of other models. This is analogous to using prefabricated wall and roof pieces to construct a house. You get to the finished product sooner, with more carefully constructed components. Unlike a prefabricated building, however, the resulting model is still completely editable at the building block level.
Assemblies have gone by different names. In original description of Stella they were referred to as "atoms," in An Introduction to Systems Thinking they are referred to as "templates," and in a more complete collation as "molecules." We chose the word assemblies to emphasize that some work putting the building blocks together has already been done, while additional work remains. We have also limited the number included in the installed software, as described in Core Assemblies to be relatively small so as not to overwhelm.
To add an assembly:
The placed assembly is part of model structure and can be edited, removed from, and added to just like any other parts of your model.
See Creating a Model with Assemblies for an example of using assemblies to construct a model.
Once you have added an assembly to a model it becomes part of the model structure. Assembly inputs are tagged (in the Documentation Tab) with the tag AssemblyInput and that tag is drawn in a light green. as set in After placing an assembly you can change the drawing of inputs from the Model Style Properties Panel. Assembly inputs are variables you will likely want to either create equations for using other model elements or replace by Ctrl/⌘ dragging another variable onto them as described in Deleting and Replacing Model Items and Data.
Assemblies are just models, and you can create your own set of assemblies as discussed in Custom Assemblies by saving models in the custom assemblies location specified in Preferences Dialog