Sure, if you like. As long as the model has the same primary sequence as
your target in your alignment file, it can be any structure.
Is it the same as using
it as a template in the alignment (that's what I do so far)? If yes, can
I define multiple infiles to model multiple loops of my protein whilst
doing homology modeling for the rest of it?
No. It merely specifies the initial (unoptimized) model. If you don't
specify it, Modeller generates an initial model by threading the target
sequence onto the template structure, and using internal coordinates to
generate an extended chain conformation for any unaligned residues. It
also differs from a template in that it has to match the sequence of
your target exactly.