I'm afraid the two terms, plus morphology, are very often confused and, as a result, mixed. In the perfect world, syntax and morphology would be two separate branches, and word order would be one of the questions syntax deals with – the main one, I should think. In the real world, however, morphology and word order are, I would say, fine, but syntax can be used for anything ranging from 'word order' to 'word order + syntax + morphology'.
Personally, I don't support this merging in the slightiest, so my suggestion would be to manually correct uses of syntax where 'morphology' was meant, and maybe it would be also a good idea to incorporate word order into syntax?