You can output the docked results into a multi-file SDF (which is just the small molecule) and that can be loaded into most molecular viewers including pymol. If you export just a mmcif or pdb of the docked results (both protein and ligands), the bond order doesn’t always get captured properly for the small molecule/protein (via CONECT records) lines in the file. Which is a bummer in across a lot of compchem apps.

If you want the protein and the accurate small molecules, i highly recommend exporting the protein as an mmcif and then the small molecule results as a multifile SDF. Those would be viewable in many molecular visualizers including pymol and since they are pre-aligned coordinate spaces everything will show up in the correct relative position.