I would like to model a protein using two templates and (!) define which
parts of the structure are modeled by which template. I.e. the core of
the structure by template_1 and a specific loop by template_2.
Modeller will use information from both templates if you give it an
alignment of all three sequences. Usually this is better than forcing it
to use information from only the one template you want. But if you
really want to do that, you do that by modifying the alignment. Align
only template_1 with the sequence in the core region and only template_2
with the sequence in the loop region.