Linux does see multiple partitions on usb sticks. But you are preparing the stick in windows, right? In win7 the driver that loads for sticks sees only the first partition on it, regardless how many exist. So you can only specify this partition as the destination. Not sure if that has changed in win8.
But anyway, since after using unetbootin or usb installer the stick will have grub bootloader, loading the install process from any partition should be fine. As long as win8 allows you this partition as destination when using unetbootin or usb installer.
Sounds like you are doing it right, not sure what's bothering it.
The long way around you could try, is extracting the ISO to a partition on the stick, and then install the grub4dos bootloader on it and create entry in the boot menu.
http://sourceforge.net/projects/grub4dos/




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