First of all you need to use an image editing program that saves transparency (transparent background). MS Paint can't do it. I've been using Gimp to do the few head merges that I have done. Are you familiar with it?
If you want a quick way that will keep all the heads lined up the way they should be to look right in the game I simply copy, paste and erase.
(1) open a copy of the heads that you're currently using, and erase the heads that you don't want.
(2) Open the bigheads that has the heads that you do want (3) copy the entire layer of heads and
(4) paste it as a new layer onto the first image.
(5) You can erase/cut any heads that are duplicated (to keep the file size down) or not.
(6) Give the file the correct heads name and save as .png
(7) If the program tells you that you need to export it first then click "yes" or "ok" whatever the case may be and you should have your new head merge all ready to put in your game.
There's probably better ways to do it but this is the way that works best for me.

Go ahead and practice, find what works best for you and whatever program you're using... just make sure you have a backup copy of your originals first of course.

Good luck!