I've no idea if this would work but it's a novel idea and shouldn't damage anything.
Try disconnecting your internal drive. Boot from a live CD, say, Ubuntu, with the USP drive plugged in. Run up GParted, can you see the USB drive? If so, set up your partitions and load them up one at a time. The boot loader should be written on the front of the first partition and allow access to each distro. Hmmm... I'm not sure if this is too simple to work but give it a go and report back.
This would mean that with your internal disk reconnected, you'd only boot whatever was on that drive unless you hit <F9> or whatever to give you the boot menu on your system. Select USB to give access to the multiple distros.
Whaja mean you're building it on a laptop/netbook and you can't get access to the internal disk!!
Build it on a desktop box then you can use it on either providing you can select the USB source from the boot menu.