Hi

you need to lookup the other ContentType and add it to a collection of IContentTypeCompositions and then assign this to the ContentTypeComposition value of the parent content type.

So for example (assuming you have a contentTypeService refrence)

List<IContentTypeComposition> compositions = new List<IContentTypeComposition>();

var myComp = contentTypeService.GetContentType(compAlias);
compositions.Add(myComp);

myContentType.ContentTypeComposition = compositions;

contentTypeService.Save(myContentType);

you can see this (and a bit more) in the uSync source - as it does this on import of content types from disk.