Hello everyone, this is a pretty interesting thread.
So it sounds like the OP has been able to get his PS3 formatted/partitioned for OtherOS (via GameOS options), and has been able to successfully install petitboot thru the "Install OtherOS" option. Awesome!
Furthermore it sounds like he has successfully initiated Fedora 12 installation and gotten up to the hard drive partitioning part of the install. At this point, here's some things you should know...
Nothing you do here to your PS3's HDD device /dev/ps3da will affect the GameOS portion of the PS3. You can go ahead and partition/format the device however you like, and you will still be able to boot back into GameOS at any time.
Fun fact: ALL Linux access to the HDD from OtherOS environment is done thru the PS3's hypervisor (this is necessary for the PS3's HDD encryption). So even when it looks like Linux is in control, the HV is actually always running too

Fun fact 2: The PS3 HV runs on its own SPU core in the Cell/B.E. in a thing called Isolation Mode which (ideally) protects its memory from access by the rest of the system... even the Linux kernel!
Anyway, hope some of that info will be of some use; will keep following this thread

Also, thanx bucanero for the shout-out to my website/youtube above; thats so awesome!
If anyones interested I recently added some new content under
http://www.ps3linux.net/development.html and
http://www.ps3linux.net/emulation.html
Happy SPUing