When the ERM100 is used in a system with a DL processor, the ERM100 is the comm master. Once it is configured it begins automatically reading from the configured slaves and will send output data to the slaves when the PLC is in RUN mode. When the ERM100 is used in a system with a WinPLC the ERM100 is more like a "proxy" comm device because the WinPLC program initiates the read and write cycles through the ERM100, the ERM100 doesn't do any automatic reads and writes.
The ERR LED on the EBC100 is most likely ON because the watchdog timer in the EBC100 has fired - because it's master (the ERM100 / WinPLC) has started talking to it then it stopped talking to it for longer than the watchdog time is set for.
The ERM100 LED being ON typically indicates errors from I/O modules in the slaves base, like broken transmitter, missing external 24v, etc.
We are not well versed in handling issues with the ThinknDo version of the WinPLC, you will need to contact Automationdirect or PhoenixConatct for tech support on using that version of the WinPLC.