Modelling domains

Hi, I have a protein with two domainswhich i would like to model. I have 3 template structures. One template (T1) has both the domains but with not good homology, which I would like to use for the orientation of the 2 domains. The 2 structures are of 2 individual domains with very high homology. I have tried to model my protein using template 1 (T1)and use the ".ini" file from it to further refine the 2 domains. Now is there a way how can i put these 2 back. Any suggestions. Or is there a better approach. Thanx, Satyan Sharma