Beginner tasked with interfacing a Cyclone III with a FTDI FT2232 USB Module

I need to create a USB interface for a black box device I'm making with a Cyclone III as the brains. I have an FTDI FT2232 USB Mini Module suited for the task. The FT2232 is solely for interfacing the FPGA with a computer through USB. I have a specific question about setting up the FT2232 to Cyclone III interface, the FT2232 supports many different configuration modes and I can't for the life of me decide which one to use. My options are: asynchronous serial UART (which I believe my boss told me specifically not to use UART so I'll ignore this), asynchronous and synchronous FIFO, asynchronous and synchronous bit-bang, fast serial interface, CPU-style FIFO, and Host-bus emulation. The above configurations were all taken from the FT2232H Datasheet which I can't link to until I have a total of 5 posts unfortunately. My FPGA configuration is active serial with ISP, JTAG, and standard POR. Ideally I'd want the simplest and most efficient interface (who wouldn't). I don't really know what I'm doing at this point but I do know before I begin I need to decide which method I'm going to use to interface them and I couldn't really make a decision I'm confident in just by reading the manual. So if anyone has any suggestions or can offer any help (on any aspects of my task as I'm just starting and had about a month and a half to finish it) I'd be very grateful. If there is any further information required please let me know. Thank you very much