About the only messing up it could do would be if you allowed it to install a boot loader to your mbr. As you have a Linux in already, i'd expect there is a Grub or Lilo already set up.
So, just formate a new partition for the install, and install it there. Make a boot disk for your existing installation first. When the new install wants to know if you want it to install a boot loader to your mbr ... tell it __no__.
Then, reboot into your first install and add a reference to the new install in your existing Linux boot loader config, as used by the original Linux install.
If you let it install a loader to your mbr, you will just have to configure it to see your other Linux, and whatever else you may have there. So, it's hardly worth it, as it is already set up.
Getting rid of it ... just ignore it, or remove the partition from the table list. Or over-write it.
A lot of people forget to restore the saved copy of their mbr, that the Linux loader would have made, when they do a final Linux uninstall. That is, they delete all of there Linux from the partition table list.
Basically, Lilo or whatever will still be there, and because it still needs the table entry to find its' second stage ... and the table entry has been removed, the whole thing just hangs.
In lilo you would be looking for a file called /boot/boot.0300 more than likely. No idea what Grub calls it. Also, in lilo you would do ...
]# lilo -u
to restore that file before uninstalling Linux. And even then, it's only required for the Linux that is providing the Loader service.
I haven't a clue as to how Xen performs is as an OS though.
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