I've been reading this document in order to check if it is possible to use both the serial communication of the FTDI chip and also control the GPIOs. I'm still unsure whether or not I'd need to control them simultaneously. From the aforementioned document there is some code to control the GPIOs, however I am still uncertain how to program the chip. What IDE should I use etc?
Yes, it is possible. In addition to the document mentioned:
See also the following document which lists the commands that can be sent to the engine.
AN 108 command Processor for MPSSE and MCU Host Bus Emulation Modes
In particular the section 3.6 Set / Read Data Bits High / Low Bytes.