There is no real 'trick' to cutting-'n-pasting heads, It's just a matter of 'positioning'.
I generally don't bother to line up the new head with the old one. I just try to place the new head so that it looks right, which usually means dropping it by a pixel or two and moving it sideways slightly.
But one thing you may find useful is to try and use a head from an attack.flc instead of a default.flc. This is because the Civ3 attack.flc heads all move slightly from frame to frame, so this gives you much more variety from which to choose from.
Here is a quick crude collection of possible shielded archers with various heads (Lonbowman, Persian, Warrior, Babylonian, Spearman and Roman.
I think that the one with the Barbarian Warriors head would make a good "Mercenary Cretan Archer"

, while the last one could be one day be turned into an "Imperial Roman Auxiliary Archer", if some of the tunic was turned to 'mail armour' by using the 'saturation down' tool like I did with that scale armour that I posted before).