Not quite sure about this, I am going from memory here, I dont run any form of M$ Windows, strictly Linux, but....
As far as I know, it is always best to use a Linux formatter/partitioner for Linux partitions, and Windows for Windows... i.e. cfdisk for Linux, fdisk for Windows...
As for a trashed "Windows" install, you might want to post, or troll, the "Windows" Forum for answers.
I have many friends that have, say, XP and at least one, to as many as three, Linux Distro's all capable of booting, on the same system. I, myself, had Knoppix and Win98 running on a dual hard drive install... From what I hear, I could be wrong, is, that, Windows should be installed first, and running, then, you go after installing your Linux. Not sure why, other than the fact that Windows cant see Linux, but, Linux can see Windows... NTFS partitions are not harmonious with Linux, if you plan to have Windows and Linux "co-exist", NTFS should not be used...
Not really sure if this has helped, but, I try
Ms. Cuddles