Johor Bahru is the state capital of the state of Johor and the second largest metropolitan area in Malaysia. Most tourists don't stop here and just pass through the city on their way to or out of Singapore. JB is a major local transportation hub however. Since it is just across the causeway from Singapore, some travellers use it as a hub to visit Singapore from here (lower accommodation prices) or to board the train, bus or airplane.
Kuala Terengganu, KT in short, is located at the east coast of the Peninsula Malaysia and at the mouth of the Sungai Terengganu (or Terengganu River) that empties here into the South China Sea. It is the capital of the state of Terengganu, which forms, together with Kedah and Kelatan, the heartland of Malay culture. KT is a good stop for one or 2 days before moving on along the east coast or towards the National Park / Tasik Kenyir.