not for sure why you would need a boot disk for XP??? but in any event, if you have a dual boot already setup, when you make a boot disk (assumming an XP boot disk), and you boot.ini doesnt include ME, you will have to manually add ME to your boot.ini. Just ensure that the 2 boot.ini's (XP & boot disk) read the same.
I have never booted from a boot disk (because the CD is bootable), but i dont think it is going to prompt you for an OS even if you change the boot.ini. It is more of a repair disk than anything from my understanding. But anywho, I hope this helps.