Quickpwn: Takes an existing iPhoneOS installation on an iPhoneOS device and modifies it to jailbreak it. In other words, an in-place jailbreak.
Pwnage Tool: Modifies an iPhoneOS device firmware file, for uploading the modified firmware to the device via the Restore process. It's more flexible than QuickPWN since you can change many things before it's ever uploaded to the phone, but it's also more cumbersome, which is why Quickpwn is how you should be going unless you have a specific reason to use Pwnage Tool.