In a much more manual version, I did this in version 1.1. I had a fan of tracks (think IRL switch yard) where I would place prints and have the bots build. The prints included a couple pieces of wood as fuel, since there never seems to be a shortage of wood. 1.1 didn't place trains in automatic, so after they were built I had to switch them to automatic. All prints included a schedule which took them out to a fuel point designed to provide the proper fuel, and to the proper wagon locations, avoiding cargo wagons, which will gladly accept fuel as well.
The decon was similar. I had another fan of tracks. There was a stacker before a single station which emptied any cargo and sent it back to the logistics network. Then the train advanced "cargo empty condition" to the fan and just sat. Every so often, when I remembered, or was making a new train, I'd use a filtered deconstruction planner to 'wipe out' the waiting trains.
Since it was all bot-based I could do it from the map view. Even before WUBE gave us "Remote view". To start the decommissioning all I had to do was at the "Boneyard" stop to the train's schedule and send it there.