If you have the same version of Ubuntu on both your USB flash drive and WUBI root.disk, then when you you use the Update manager, it will update the “Grub Menu” so that you can boot into either your USB or WUBI install of Ubuntu. I discovered this by accident! This is a useful tip, because the only other way you can boot into a USB install of Ubuntu is a change your machine’s BIOS settings making the USB flash drive the highest priority boot device. However, if you do this, it means that any flash drive that happens to be plugged into the machine will be booted, if it is bootable. You may not want this, so that’s where this tip comes in.
Explanation: on a Vista or later windows version computer, the boot procedure is not the same as it is under Windows XP and earlier. When you install WUBI on a Vista machine, it makes an entry in the Vista startup menu items allowing you to select either Windows or Ubuntu. If you choose Ubuntu it takes you to a second “Grub” menu, which in turn takes you to your Ubuntu installation. If there is more than one Ubuntu start disk attached to your system, then Ubuntu cleverly adds an entry to this list. So you can choose to boot from either the USB flash drive or the WUBI version. In this way, you can add as many Linux distros as you have USB flash drives!