Okay, I just loaded my version of Shades of Atlantis to double check the proper installation of the character set.  There are no additional morph sets required.  Usually when I apply an injection pose or morph, I double click the icon in the Library.  Clicking on the check mark at the bottom of the Library will accomplish the same thing.  The only feature that will change on M4 is his face.  There are no body morphs; those will need to be injected from a different pack.  If you are still having problems, post a before and after image so I can narrow down a solution.