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If I burn to disk will I have to use the boot cd every time
No, you should only have to run the installer disk once.
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will I be able to save to my Xbox HD?
Yes, you should be able to use your hard drive on your xbox.
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Do I have to FTP in order to get AID onto my HD?
the question you ask about ftping is a little more complicated than a yes or no answer. You have to use a disk to install programs on your box with the xchip, it does not have a built in ftp program on it. to use your A.I.D. you will not ftp in the beginning, but you will have to ftp in order to complete your install from your A.I.D. disk. Your auto installer delux should have come with a pdf file. E.B.2.K. has a bunch of pdf files. Most of what your looking for will be found in there.
burn the iso to disk and cold boot from dvd tray. make sure you have the correct bios placed on chip to ensure that your installer disk will boot.