I believe you are referring in terms of FX2LP. FIFO and endpoint buffer is essentially the same physcal buffer. It is called as endpoint buffer when the FIFO is under the control of USB domain, else Slave FIFO.
It depends on which mode FX2LP is configured to work (auto/ manual), whether the data written to Slave fifo goes to EP buffer directly or not. In Auto mode, the data written to Slave FIFO is automatically committed to USB domain(the control is transferred to USB domain); i.e. is accessible as EP buffers. In manual mode, it has to be explicitly committed.
I believe it would be clear with the AN http://www.cypress.com/?rID=12926.