You don't need Putty, you can SSH into your iPod with Terminal.
To do so, open Terminal and enter-
ssh -l root 123.456.789.123
(but enter your iPod's IP address instead of '123.456.789.123')
It will ask you for the root password for your iPod, and then you're in and can enter the actual commands to modify your directories.
If it all goes to pot, you can always restore and re-jailbreak. But you should be just fine.
You don't need Putty, you can SSH into your iPod with Terminal.
To do so, open Terminal and enter-
ssh -l root 123.456.789.123
(but enter your iPod's IP address instead of '123.456.789.123')
It will ask you for the root password for your iPod, and then you're in and can enter the actual commands to modify your directories.
If it all goes to pot, you can always restore and re-jailbreak. But you should be just fine.