えんえ should be en'e according to the govenment system. ティ is used exclusively in loan words anyway as far as I'm aware. Wouldn't you just write it in its original language?
(you probably know this but) zu du and zi di do make a difference in terms of which kanji are used. The government has been reforming kanji readings over time though E.g. 藤 ふぢ → ふじ or 図 ヅ (look at the character in the box!)→ ず
