The FX2 can be configured in either GPIF or slave FIFO mode by setting bits 0 and 1 of the IFCONFIG register as follows:
It can only be set in one mode. The part cannot work in both the modes at the same time. Please refer to page 13-11 of the Technical Reference Manual for information on the pin assignments and functionality in these different modes based on the IFCONFIG register bit setting.
Your firmware can dynamically switch from one mode to the other by writting write to the IFCONFIG register accordingly. In this case you need to make sure that the external device with which the FX2 is interfacing is designed to take this mode change into account. Note that he pin functionalities switch depending on the IFCFG register setting as per table 13-10 of the TRM.