As far as where to format it from, there is really no difference assuming both choices use the same version of Disk Utility (that is unless the disk is Leopard and the HD is Tiger for instance). Always use the latest version of Disk Utility.
As far as the length of time, I don't believe I have ever seen it take over a minute and most times less than that. If it taking substantially longer than that (like giving you enough time to post about it 🙁) then Disk Utility must be hung. I hate that as force quitting DU will leave a disk like that in an unknown state. Usually just restarting the drive after the force quit will set things right again so you can try again to format/partition it.
BTW- Since you have a G4, when you repartition it be sure to check the "Options" button at the bottom once you have set the partition names to make sure "Apple Partition Map" is selected- then proceed with the partitioning.
