Jailbreaks are not stored on the PS3. That is why you need to connect your iPhone or USB device to the PS3 everytime. So if you insert your iPhone to jailbreak, the next time you start the PS3, nothing is saved and the PS3 starts as if nothing happened. You only overwrite your PSFreedom is if you overwrite it on your iPhone.
Hermes and PL3 both are slightly different. Both have pros and cons. Hermes seems to be supported more and a preferred choice.

