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1. Format the pen - usually it's just:
fdisk /dev/sda (assuming the pen is 'sda')
-- create a single partition
-- format the partition as ext2fs
-- use 'tune2fs' to switch off the features to run fsck on the stick
2. Create the /boot directory on the partition
-- copy the initrd and kernel from the CDROM
-- if you're using GRUB, set it up on that stick (lilo is actually easier)
3. Install and configure the bootloader (grub or lilo)
4. Test boot the stick and hope it runs
I have never looked at a Puppy iso file so I don't know if it boots and remains in the initrd. If it actually does a 'chroot' to another filesystem (whether uncompressed from another file into RAM or read directly from the disc), you will need to copy these other files to the usb stick and put them in a location where (hopefully) the boot scripts will find it. Usually this just means copying the structure of the cdrom - for example, if it has a directory 'extra/other_files' then make a copy with the same hierarchy onto the USB partition. If the boot scripts just don't find things and get confused, then you have to take apart the initrd, edit scripts, and reassemble the initrd.
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