Rome to Assisi

Annon,
We were there last spring. Took the regional train from Rome to Assisi. Ride took about 2 - 2 1/2 hours. The train was not in the station proper but at a track about 750 yards out. Almost missed it! There are a number of non-stop trains and some that you must change in Foligno. Your choice.

When you arrive you can purchase bus tickets and take the bus up into town.

Use the RS guidebook and take the stroll through Assisi.

Our favorite hotel is the Hotel Ideale and restaurant is Trattoria da Erminio.
Enjoy you time there. It's a really neat little hill town. Plenty to see.
Gene

There are only two buses per day from Assisi to Rome, versus almost hourly train options. How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it. Trenitalia.com is the one that sells train tickets, but I prefer to read most train schedules through the first link.

Annon,

If you'd rather not have a change, there are direct departures from Roma Termini to Assisi at 07:58 and 14:23. Travel time will be about two hours with those, and slightly longer for the routes which involve changes. When you arrive at the station in Assisi, you'll have to use Bus or Taxi to get up the hill (details in the guidebook, as I recall).

The trip from Assisi to Marseille is going to be considerably longer. Travel by train on that route is going to take between 13 and 23 hours, with multiple changes. One way to minimize the long travel by train would be to make an intermediate stop for a night or two.

In the same situation, I'd probably return to Rome / FCO and use a budget flight from Rome to Marseille (flight time about 1.5 hours). Some of the airlines you could check are Vueling, Alitalia and RyanAir. You could use a train departing Assisi at 08:30, arriving FCO at 11:07 (time 2H:37M, two changes). There's a more direct departure at 07:03, arriving FCO at 09:52 (time 2H:49M, one change).

Thanks to all for very helpful information!

I agree with Ken that going from Assisi to Marseille, I'd fly from Rome to Marseille. Look at Skyscanner for all your options on this route: http://www.skyscanner.com/