I set the boot order to (1) USB Hard Drive; (2) USB CD/DVD Drive; (3) USB Floppy 😮 ; (4) Hard Drive; (5) Network Drive... well something like that - I don't remember there being 5 options actually. Essentially, anything that began with USB I placed in front of my main hard drive. I got the same result whether with the flash drive or the 2.5" SATA drive connected via USB cable. The flash drive is formatted FAT32, the SATA is NTFS.

If I use a smaller flash drive that already has something on it but has more than 1gb free, will UNetbootin make a folder and keep Puppy separate without me preparing the drive in any way?

I'm elsewhere for a while now, see ya later :)