If you are the one doing the hardware, than you should provide on the PCB one JTAG connector and another connector for a serial port. These two connectors must be on all boards, not only the development ones.
The JTAG is used to program and/or debug all chips supporting JTAG from your board (all at one JTAG connector only, so you can access them without switching connectors or jumpers). The COM port (serial) is used to send receive whatever data you need, for example to talk with the UBOOT or to SSH in Linux, etc.
A single FTDI chip can provide 2 "channels" (see the datasheet), that is why both the JTAG and the COM interfaces can be handled by a single FTDI. This dual function is not critical, one can use as well two distinct programming cables, one USB to JTAG and one USB to serial.
That is why two connectors are needed, one JTAG and one serial connector (just the pins from the serial port of your chip, not the +/-12V RS232 level buffers like in a PC, but the same voltage as the rest of the JTAG, unless it was specifically requested to be RS232). However, the connector's holes are needed on all boards. You can leave the connectors unpopulated for production boards, and use pogo pins to program them, or use preprogrammmed chips, but the JTAG and COM holes must be available on all boards, development or production.
The FTDI chip with the USB (JTAG+COM) is usually sitting on the programming cable, not on the PCB. You can either buy a FTDI JTAG cable and reprogram it, or make your own FTDI to JTAG on another small board attached to an USB cable, for the FT2232 alone.
What you see on devboards, where the FTDI chip (the programming cable) is included on the same PCB as the demo chip is an anomaly. That method is used for learning purposes only, because the student might not have a JTAG cable and might not know how to connect it to the board (some JTAG cables have DUPONT wires you plug one by one in the JTAG pins of the board).
You can always buy a ready-made JTAG cable for whatever processor or FPGA you are using, otherwise you will need to "steal" the EEPROM content for your JTAG, because most of the proprietary IDE/toolchain will accept only their proprietary JTAG cable. Do not use stolen software for your job. Buy the darn cable and forget about the FTDI part. Just add the two JTAG and serial connectors on the board, that's all.