First, do not go by what people say about other Linux OS.
Puppy is Puppy Linux and does things the Puppy way and for good reasons!!
If you did a
frugal install of Puppy version.
It uses a save file or folder to store any changes or added stuff.
The core operating system files/programs stay read only.
However, stuff in the save can modify how they run and load into memory.
When everything is working correctly.
If you make a simple copy of the save.
That is a good backup.
If something goes very wrong.
Simply replace the save with your save copy, reboot, and everything is back to normal.
I usually add bak. to the beginning of the name of the save copy to keep it from being seen at boot up.
To make it a working save, simply remove bak. from the name.
Add new stuff you want to keep.
Make a new copy of the save.
The big deal about running as root is on systems that you have multiple users. You want to restrict what they can do.
Keeps the dumb people from making changes to the system that break it and give tec support problems to solve all the time. However, these dumb people do not do anything but run a program. They only need to be able to do only that.
It takes someone running as root to add, remove programs, and make system changes.
That is always going to be you, so just run as root all the time.
Puppy is a one user system.
You want that user to be able to do it all.
The only option to restrict what can be done is to run a program as spot.
The idea of spot was to limit what Internet programs can do.
Web browsers specifically.
About root, spot and fido
http://www.puppylinux.org/wikka/spot?redirect=no
Fido was an idea still in testing and development, so it may or may not be offered in the Puppy version you have.
My limited use of it was, why am I using this?