Well if you're using the standard graphical installer I don't think there is any way you can change how grub installs, but with the alternative one there should be an option for advanced package management or something. So if you're using the default installer I would take out (or better yet just disable) the internal HDD just in case.
Alternatively if you don't want to fiddle around with the internal organs of your PC, just restore the windows bootloader and reinstall the grub bootloader on the external disk after you have successfully installed ubuntu (if you're lucky it might not even install grub on the main HDD).
If you manage to mess things up just google SuperGrubCD, it's a life saver when you need to sort out bootloaders & stuff.
And one more thing - what's wrong with having grub as the bootloader? /