In the Protein panel you can select a PDB file to be used. That PDB file will be loaded and analyzed using the pdb2adf program. This means you have to make sure that 'pdb fragment files' are available for each non-standard residue, as required by pdb2adf. With the controls in the Protein panel you can select which Amber type to use for the different residues, and what residues and / or atoms to put in the QM and MM regions. You can also add a solvent to your calculation. Next, you can use the QMMM panel to set up other technical details of the QMMM calculation.
Currently, the protein is NOT further integrated with the molecule editor. Thus, you can not use the edit tools to change atoms in the QM or MM region. You will need to edit the PDB file.