The installer will configure everything, so do not worry about the pinout stuff, that is there in the manual just for your reference.
What you are describing, is that the board is seeing a servo fault. Which I think is normal as probably you have not tuned the servos yet. Set DIP4=off to disable servo fault detection to force the servo to remain active while you tune it. Once you have tuned the servos and they are OK, you can turn the servo fault detection again.
Arturo Duncan
https://cnc4pc.com