S&M, they all run on the same tracks. As you approach the stations, the tracks muliply a bit so that the faster trains can zip through places where they don't stop. In larger stations, you will have multiple platforms and lots of tracks.
Depending on where you travel, train changes between the different categories of trains is highly likely. The ES, EC and AV trains just don't go to many, many smaller towns and cities. Thus, you may be on a ES for part of the journey and you could then change to a R train to get to a smaller town. If you did a trip from Florence to Lake Como, you would see that type of train run.
By the way, the fare on an R train is often 1/2 that of a Eurostar. For example, the Rome to Florence ES. It's non-stop and takes 100-min. It costs 36.10Euro. Instead, you could take regional or IC trains that stop everywhere along the way and pay far less. But, your trip would take 3-4 hours. Same tracks. Your choice.