In any/all case(s): the center of mass is the vector sum of the position vectors of the marker points. If you want to find the center of mass position vector with all markers included, and want to retain this position vector even after you do not include all markers in your analysis, then do so. I do not recommend you doing so. Formulas involving center of mass vector position assume that all markers are included in the analysis.
If, on the other hand, you want to find the coordinates of the marker points you did not include in your calculation of the center of mass position vector, then just drag these along in your coordinate transformation. That is okay. Just don't include these other/dragged marker points in the analysis (but display them in graphics).
Did I interpret your question correctly? Kind regards
I'd try to build the muscular skeletal model first with all the markers visible, then calculate the center of mass of each limbs. I'd recommend Opensim. https://simtk.org/project/xml/downloads.xml?group_id=91