Halliday & Matthiessen (2014: 490-1):
Whereas parataxis and hypotaxis are relations between clauses (or other ranking elements), embedding is not. Embedding is a semogenic mechanism whereby a clause or phrase comes to function as a constituent within the structure of a group, which itself is a constituent of a clause, e.g. who came to dinner in the man who came to dinner. Hence there is no direct relationship between an embedded clause and the clause in which it is embedded; the relationship of an embedded clause to the ‘outer’ clause is an indirect one, with the group as intermediary. The embedded clause functions in the structure of the group, and the group functions in the structure of the clause.