I just wanted to report a bug, which is a NullReferenceException on SaveChanges when adding a new Taxon to Subtaxa in a custom hierarchical taxonomy.
The workaround is to set the Taxonomy property on the new Taxon (this is not in described in the documentation examples). I experienced this problem with version 5.4.
teacherTaxon = taxonomyManager.CreateTaxon<HierarchicalTaxon>();
teacherTaxon.Taxonomy = teacherClassesTaxonomy;
teacherTaxon.Name = teacher.Username;
teacherTaxon.Title = teacher.TeacherName;