To merge two molecules, you can add a bond betwwen two atoms, one from each molecule. The drawback is that this method will not align properly the two parts of your new molecule.
Another and much better method is to use the Merge button:
Suppose you want to draw a naphtalene molecule starting from two benzene molecules:
Move one of the molecules so that at least one atom from each molecule lies at the same place. These atoms must be identical (same element). In the examples, two atoms and a bond conincide:
Then, select the two molecules. The Merge button becomes sensitive. If you click on it, you obtain:
If one of the molecule has two or more atoms at the same position than an atom of the second molecule, the result is not easily preditable.