As you test larger circuits, you will likely find bugs. To nail down what's going wrong, exploring what's going on in the subcircuits while running the overall circuit can help. From viewing the overall circuit, you can do this by bringing up the subcircuit's popup menu (right-click or control-click its box). Then choose the View option.
After choosing this, the view will switch to the subcircuit.
Notice that the pins' values in the subcircuit match the values being sent to them in its containing circuit.
While in the subcircuit, you can change it however you want; any changes to pins' values will be propagated within the containing circuit. (If you attempt to toggle a pin using the Poke Tool, Logisim will pop up a dialog box asking whether you want to create a new state; responding Yes will divorce the state viewed with the subcircuit from the outer circuit's state, while responding No will cancel the toggle request.)
Once you have completed viewing and/or editing the parent circuit either by double-clicking it in the explorer pane, or via the Go Out To State submenu of the Simulate menu.
Next: Logisim libraries.