usually/ but not limited to when you want to boot from a device,
be it the floppy, cd-rom/dvd-rom/ writers,USB device (can be
thumbdrive, USB card readers, USB ext drives etc),it is to execute
another program that works beyond the windows registry of the
existing partition.
if you want to format your hdd you can choose to boot from cd-rom
if you have the windows or recovery cd for your pc.
if you want to recover another partition or work on it and if you
have created rescue diskette for it you can boot from the floppy
and the program will be executed afterwards.
do you have a installed a complete OS in the USB hdd? are you
trying to run another OS other than your existing copying at the
IDE hdd?
if you got nothing to boot into from your USB hdd (no OS, no 'live'
programs, no rescue function) then of course after reading the USB
device the computer will boot into the OS you have in the IDE, or
restart/ shutdown if you have no IDE there after to Boot into
another OS.