R = Regional train - will only have walk up fares and most people won't reserve their seats - just get on and sit anywhere. A bit like catching the subway or a commuter train. It will be easier if the train starts in Milan as you'll get a seat if you arrive early enough; if you have a choice, avoid trains that have come from somewhere else e.g. Torino).
IC = Intercity train - may have discounted fares. As stut says, you need to check the prices and see if there is more than one fare quoted (mini, base, flexible). If there is more than one quoted, then the lower one is discounted. If not, then either all the discounted ones are sold out, or they only have walk-up fares on that route.