Is there an *explicit way *to tell modeller which residue (in the
template) must be aligned with which residue in the sequence?
Yes, this is what your alignment is for. If you align residue X in your
target with residue Y in your template, that's what you'll get in your
output model, end of story.
I'm looking to keep the structure identical in some segments.. and have
modeller make a best guess in other parts.