Yes, the two serial ports are correct.
Yes, this is most likely the issue. You need an ELF file. Then you can start up gdb and point to the elf file:
You start gdb and point to the elf file:
arm-none-eabi-gdb 'elf file you want to flash'
Now from GDB, you can connect to an attached device. Attach the JTAG cable to the target. But you need to tell GDB where to go, so let's point it to the serial port:
target extended-remote /dev/cu.usbmodemJEFF1
(I'm not sure what the destination is on windows, but replace /dev/cu....)
Then tell the probe what kind of JTAG you want to use, probably 2 wire serial:
monitor swdp_scan
Assuming you see the target, you can attach to it:
attach 1
Then you can load the file:
load
You can now walk through and step through various aspects of code, assuming the elf file has debug symbols in it. We're going to start diving into advanced firmware topics, and I'm not sure your experience.
Here is the documentation, for the same product the firmware is derived from: https://github.com/blackmagic-debug/blackmagic
They have a lot of documentation, and a wiki to get started.