[modeller_usage] Using my own initial structure to model a loop

I was looking at :

http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel

and was wondering if it's right to pass a loop fragment generated de novo into automodel with the inifile parameter. 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?