As Ramhound and Techie007 said in the comments, it really doesnt matter where you put it... with a few exceptions.
With any device you attach to your computer, internally or externally, just make sure it doesnt impede the operation or placement of other devices. Problems that could occur is stretching cables or putting pressure on an internal card.
There are other things to consider, such as airflow and heat. Some cases are designed to allow air to flow along a certain path. Generally, they take new drives into account, but it cant hurt to check.
Another factor is sound. Depending on how the case is made, putting the drive in one bay over another might make it vibrate more and sound louder.