Do you mean I somehow need to connect all the yellow circled pins together? When do I do this, just before or after the FTDI is connected? Then what?
This all yellow circled pads are for ISP programming. Bootloader is a small program that listens on TX/RX pads and allows programing through FTDI chip. But chip from manufacturer comes empty, you need to put something on it. Either a program or a bootloader. So this is what ISP port is used for, which allows you to program the chip directly.
You need to google for how to flash bootloader to minimosd with arduino. You can try first updating bootloader on it and then flashing firmware, as described before.
Minimosd is nothing else than small arduino. There are two ways to program it, via TX/RX if it has bootloader or via ISP port (which can be used to flash bootloader).