I´ve never tried it, but:
I´d ready a pendrive and boot ubuntu from it running it live to see if all works as expected.
Alternatively you can burn the iso to a cd and skip the quote below.
After having booted into the live ubuntu, I´d plug in the USB HDD and simply install it from there using the live ubuntu itself, write GRUB in the MBR of the USB HDD and on next boot, simply boot from the usb hdd.
I guess you´r asking this because you got no room on your hdd for an ubuntu partition, however, you can resize mac partitions as well on the fly without using data, but you need to use the console =)
If you got a fast Pendrive it got a very good performance and if you got a windows at hand you could set it up with USB Pendrive Installer and run it there with a casper file system to store your personal stuff, then its a live ubuntu from a pendrive, where you can install your stuff and store your settings, which has the advantage, you always got your working environment in your pocket.
I´d also recommend using a windows machine and the pendrive installer prepping the pendrive for install, rather than using the mac commandline - its prone to error