A tool that can flip the bit and should work with most usb flash drives is Lexar’s USB format tool. It is a portable tool that has been designed for Lexar USB drives but it works with other brands as well. The main interface can not only be used to flip the removable bit but also to format the usb drive, set a volume label and a partition to be bootable. You only need to press the flip removable bit button if you want to prepare the flash drive for use with multiple partitions. The drive has to be removed and connected again to the computer system afterwards.

It should be noted that Lexar USB Format (via Shell City) will not partition the usb flash drive which has to be done with other tools. For that you can use the build in tools in the operating system. Read Joshua’s System Partitioning With Vista article to find out how to do that in Windows Vista. A more universal software is the gParted Live CD which can be booted from any computer system.

Another option to create multiple USB stick partitions has been discussed before at Ghacks. The process involves editing the Windows Registry and has the disadvantage that the add-on partitions are only visible on that computer system.