T
@dsurname it's now a bit offtopic from the thread description, so please start a new topic which will better describe your issues. At first, you do not need to worry about the RUN led. If you try to read a DI, the behavior of RUN led will change.
/dev/ttyAMA0 is the UART of RPi, not the RS485 of Neuron. If you want to access the RS485, you need to install UniPi drivers (currently is part of in Evok https://github.com/UniPiTechnology/evok, in future, there will be Debian packages). Once installed, the RS485 ports are will be available for example at /dev/extcomm/0/0