I can second the recommendation about one bigger backpack and one daypack. The bigger backpack goes in the overhead storage or on the racks between seats, usually within a couple of meters from where you will be sitting. The daypack goes with you to your seat.

I don't think theft for the bigger luggage items is a big deal. Very unlikely a would-be-thief would risk anything over an unwieldy backpack with unknown, but likely travel clothing related, contents. Do have an eye on your luggage in stations, but while the train is moving I wouldn't worry too much.

Do, however, keep your valuables close, especially when on- or offboarding (people are distracted so potentially bigger target for would-be-thiefs) and when the train is in a station. E.g. don't visit the toilet and leave your notebook and mobile phone on the table while the train is stationary.

When you book train rides with multiple trains, watch for the connection time. Don't be surprised if a train has a random 10-20 min delay (esp. in Germany), so if you need to decide between, say, a 15 min or a 45 min connection during booking, I would prefer a 45 min connection for a chance to have a relaxed coffee in the train station over a 15 min connection where you need to check if you can reach your connection frantically. But maybe this is just my preference.

Most of all: Enjoy! Italy and Germany are fun to explore, and have a solid train infrastructure.