Section 9.2.7 of the Technical Reference Manual provides a step-by-step sequence that the master requires to write to the SLAVE FIFO. Following this sequence will ensure that you are meeting the timing (hold and setup) as stated in section 9.9 of the EZ-USB FX2 Datasheet.
You may change the FIFOADDR lines anytime to address a different FIFO. However, make sure that you abide by the FIFOADDR lines hold time with respect to the activating edge of the SLWR as stated in 9.15 of the datasheet. As long as you meet the setup timings of SLWR, FIFOADDR and FD, as per the datasheet you should be fine.