Probably the easiest way is to save your custom head as two separate files, one for the neck and one for the head then edit the Apollo CR2 file to call them up. The CR2 lines should look like this:-

actor chest:1<br></br>
    {<br></br>
    storeageOffset 0 0 0<br></br>
    geomHandlerGeom 13 head<br></br>
    }<br></br>
actor neck:1<br></br>
    {<br></br>
    storeageOffset 0 0 0<br></br>
    objFileGeom 0 0 :Runtime:Geometries:Your
Folder:neck.obj<br></br>
    }<br></br>
actor head:1<br></br>
    {<br></br>
    storeageOffset 0 0 0<br></br>
    objFileGeom 0 0 :Runtime:Geometries:Your
Folder:head.obj<br></br>
    }<br></br>

The original head morphs will naturally not work with your new head but doing it this way you'll not mess up morphs in the rest of the body.