See this post for instructions for how to take stuff that's on a bootable DVD and placing it on a USB drive that's bootable.
A USB Thumbdrive is just a hard drive, and if it's got the right boot files and the BIOS supports booting from an external USB hard drive it will work fine.
To understand what makes a CD or DVD drive bootable see this post on the El Torito (CD-ROM standard).
Regarding the bootmanager: when using FAT as filesystem then syslinux would be one approach. Especially when booting from USB you might consider using grub for booting, as you'll be flexible with the grub shell (providing a nice tab-completion). To install grub you'd be running something like:
mount /dev/sdX /mnt/
grub-install --recheck --no-floppy --root-directory=/mnt /dev/sdX
and adjust /boot/grub/menu.lst accordingly.
Your bootloader has to load kernel and initrd. So those files have to be outside your debianroot.img (unless you're using the ISO approach and grub2 with its loopback option, see http://michael-prokop.at/blog/2009/05/25/boot-an-iso-via-grub2/) and need to be referenced/configured in your bootloader (being syslinux.cfg for syslinux, menu.lst for grub1 and grub.cfg for grub2). The following is an example menu.lst file used for the grml live system (http://grml.org/) generated by grml2usb (http://grml.org/grml2usb/):
# misc options:
timeout 30
splashimage=(hd0,0)/boot/grub/splash.xpm.gz
foreground = 000000
background = FFCC33
title grml - Default boot (using 1024x768 framebuffer)
kernel (hd0,0)/boot/release/grml/linux26 apm=power-off vga=791 quiet boot=live nomce live-media-path=/live/grml/
initrd (hd0,0)/boot/release/grml/initrd.gz
The initrd file has to locate the debianroot.img on your devices and loopback mount it then. Then it should change your root file system via e.g. pivot_root (see http://linux.die.net/man/8/pivot_root) to inside the mounted loopback file. You can find more details regarding the initrd process in Documentation/initrd.txt of the linux kernel sources: http://lxr.linux.no/linux/Documentation/initrd.txt
If you'd like to know how common live systems do this kind of stuff check out debian-live (http://debian-live.alioth.debian.org/) or grml-live (http://grml.org/grml-live/) in combination with live-initramfs (which does all the initrd/initramfs magic and is used in most Debian based live systems; http://packages.debian.org/sid/live-initramfs).
A different approach to your debianroot.img approach would be talking an existing Debian based Linux Live system providing so called "root persistency" (for example the official Debian-live project provides this as well as grml 2009.05 does).
Best Answer
Use BartPE to make a minimal environment you can boot from USB media, and from there you can prepare your windows installation and run the appropriate installer.
http://www.nu2.nu/pebuilder/
Once you have configured your BartPE image, and sent it to your USB drive. Go ahead and reboot and issue the following command:
Where D: is your USB drive, and C: is the hard drive you want to install to. Just walk through the various prompts etc.