When ive dual booted normally with drives installed to play ie linux or vista ,(other windows based installs are simply removable from the boot ini) The base of is always XP. Both linux and vista have there own boot programs which can be cleared by the fixmbr command in operating system recovery(normal might screw you up if yoru not careful warnings) The safest way is with the caddy but good alu ones are expensive
Of course just having a recent ghost image of primary hdd as long as this is system will also wipe all other boot sector configurations