If you have a Molecule Window open containing the structures and a sequence alignment window with their linked structures, you can select the residues that you want to superimpose by either selecting them in the Alignment Window or the Molecule Window. Then click on the top of the Molecule Window so that it is the active window (make sure you click on the top so you don't change the selection). Then within the Macromolecules toolset, go to the Superimpose Proteins tool panel. The default settings should be "Superimpose by: Sequence Alignment", and the Reference Protein and Sequence Alignment values should be already set (if not you can set them). Then you just need to click the Superimpose button at the middle of the panel (above 'View').

The attached video illustrates this process with a few extras. It shows how you can select a ligand in one molecule and then use Edit > Select to select residues within a radius of the selected ligand. Then in the Sequence Window it uses the context menu's Extend Aligned Selection to expand the selection to the aligned residues in the other sequence. The Superimpose command then superimposes based only on those selected residues not the entire alignment. What you end up with is a structural alignment of just those selected residues.