It is vitally important for their understanding of chemistry that they understand that molecules are three-dimensional things and that they have a spatial requirement in that they have a shape of their own and that shape will change. They can't do higher level manipulations without an understanding of three-dimensional nature of molecules.
Use small group student-centred interaction using structured work sheets that logically develop students' conceptual understanding. It’s a learning cycle approach.
Students’ ability to visualise the molecules in free space is limited sometimes. So a strategy is to ask the students to take out their smart phone and use it as a mirror by putting it opposite the molecule on the paper, so that they can see the reflection and easily visualise the molecule. This is good for teaching enantiomers and rotating the molecule.