The train system is cheap and effective in Morocco. I have used it to travel between Rabat, Marrakech, Fes and others regions of the country.
Finding out the schedule is simple through the ONCF (the train company) website.
When the results come up, one column says 'Correspondance'. That means at the station listed, you have to get off at that station, and transfer to another train.
From what I have seen, the trains have two main classes: First class and Second class. The price difference can very from as little as 40dh to 100dh and over. In both classes, there is air conditioning and you can lift the arm rests up to lie down if you're lucky enough to have a row of seats to yourself. What first class and second class can look like in different trains vary in terms of seat appearance and positioning.
First Class: These tickets are pre-assigned. You are guaranteed a seat. As you will see in the photos below, the seats are cushioned and spacious. There is much more leg room than in second class. There is enough overhead space for you to store medium sized luggage. More ONCF workers are going back and forth on first class. So if you tell them to alert you to your stop, they will.
Second Class: Second class costs less, but also has air conditioning. Seating is based on first come, first serve. They seem to oversell the tickets because people will be standing in the aisles. The luggage space is also very minimal, which sometimes means we travelers are left with no choice but to annoy the locals by blocking alley way space with our luggage, and it gets embarrassing. The leg space is also tight. At times you are knee to knee with others. If you want to guarantee yourself space and especially a place for your luggage, no stress, take first class.
The train stations are very modern and beautiful, even in the most rural areas. At the station you can easily buy your ticket 30 mins or 15 mins before the train arrives. The tickets are sold at counters, or automated machines. Often there are ONCF helpers standing around who will process the purchase for you
When at the station, you have to look at the LCD boards for your train. It will list the Destination, Time of Departure and also the train number. Unfortunately the ticket does not list the platform, so you just have to check the different boards or ask someone which platform has the train to Fes, for example.
As for the stopover, Have you ever used a subway? Sometimes the train switch is as easy as that. All you have to do is get off one train, and figure out where your platform is for the next train and walk underground and over to the next platform. There's always staff hanging around who can assist you. Just show them your ticket, and they'll tell you the platform number. There will be clear signs directing you to that platform. At that platform there will be signs that list the Destination, Departure Time and Train Number.
There are toilets on the train.