There are full mechanical drawings on my website, including the io connector positions.
The USB on the left is for flashing the ARM only, usually you would use soft-update.
The LEDs are visible through the back panel.
The 5V 2 pin header can either be used to feed in 5V or drive an external LED (with a resistor).
I have suggested using the io patch panel to drive copies of dsk and pwr LEDs, so we can come up with a standard for that.
I can fit a header there as an option, normally it is unpopulated.
The power switch on the back would be left in the "on" position if it's in case, and either the 5V supply switched, or the ATX power control PCB can be used to switch on/off an internal power supply using the case power button.
/MikeJ