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Edit: Also lets keep this thread about the kernel and bootloader, we can figure out where to put the rootfs later.
DJ_O that is out of scope of this thread. Once we have a working kernel we can decide those logistics but without the kernel any other speculation of how things will work is pointless. But in response to your question:For booting Linux on a Windows Mobile device you can either install linux to replace Windows Mobile or you can use what is called a chain loader to boot Linux from Windows Mobile so that you can still use both, we'd most likely go with this second option.