When you boot from a CD or Stick to Puppy, It doesn't affect your local computer. However it does mount the hard drives so you can read them. They will show up at the bottom left of your desktop as SDA1 or SDA2 etc. You can open these, copy the files, move files and pretty much do anything you could with any other operating system. Just don't modify root, or windows system files and your fine. I use puppy as a recovery OS. I boot a machine that wont work to puppy, copy the files off onto an external Hard drive or stick, then I can do some repairs (Replace bad or corrupt windows files etc), and reboot the machine. Worst comes to worst, I can format the OS and reinstall windows then copy their data back on.
Just don't run the "Partitioning" programs in the utility directory. Everything else is sweet.