I have never used the DDR2 MIG IP core, but as I understand it from Pg16, ug388.pdf, from the block diagram I see that internally it has command (CMD FIFO *) and data FIFOs (32 bit bi-/uni-drectional).
Then I have this excerpt...
FIFOs are used at the User Interface of the command path and datapath to queue up memory requests and to manage the transfer from the user clock domain to the memory controller clock domain.
As I understand it, it means that FIFOs exist just immediately after the user interface ports inside the MIG core.