This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
When you call close on the Connection instance you got from the pool, it usually means the connection gets returned to the pool and can be reused (it depends on the connection pool implementation, but I'd be surprised to find a connection pool which would do something different).
You might also obtain the physical connection (at least with some pool implementations) and close that one. However, the pool probably won't know what happened and will try to reuse the connection if you return in to the pool afterwards, in which case the next user of that connection will get an error (sometimes the pools verify connections before handing them out). However, there is no good reason to ever do something like this.