Label protein strucuture residues in Chimera
You cant do this in Chimera, but in pymol you can write a script to do this. 

In terms of the view, you can use get_view on the command line. This returns a section that you can copy and paste in - which will give you the same view every time. I recommend labelling the residue you want, then finding the position you want to view it from. Then using get_view to get that view, which you can use every time (just copy it into a text file) for a reference

This does presume your different molecules are aligned, but you can do that in pymol as well to make sure that when you use the output of get_view it is consistent.