Both are good books, but you would have to spend a LOT of time underground to get full use from a book that details as large a space as The Underdark. Underdark overall has more stuff ( more races, more cities, more geography ). Serpent Kingdoms has some of that too of course, but I'd say more detail on what it does cover. Serpent Kingdoms could definitely be a great resource for detailing an ongoing serpentine campaign menace in Eberron.
You really can't go wrong here though. It's really more of a stylistic question for you to answer yourself.
edit: The Underdark was released right before the 3.5 update i think...