I found panels highly non-intuitive, but got there with much persistence and head-scratching. I have JMRI auto-booting on a Raspberry Pi underneath the railway, and I control it from Digitrains on my phone. I've only got points manually laid out on a panel at the moment, which loads with JMRI as it starts - routes will be later.
Having said that, SPROG3 and JMRI and a Pi works very well.