assign multiple templates

Is it possible to assign more than one template without alignment by giving the pdb IDs? My protein has 5 repeating domains and every domain has its own pdb file. The automatic option without assigning a template just found one of the pdb files and also just predicted one domain correctly - the other show significant deviations. I know the secondary structure of my protein, but wanna know the tertiary structure. My protein contains mainly helices (at least 15) and the predicted model I just contains one helix and many beta sheets. How can I help the server in the prediction?