While trying to wipe a drive with DBan I accidentally started the process on my laptop drive. The process ran for about 2 seconds before I stopped it but not before it caused some damage. I now have an unallocated file system so windows can't boot. I've loaded Ubuntu from a USB stick to try and get to the drive. I want format it to NTFS and I'm given the option to "Don't overwrite existing data(quick)" will this mean it just sets it as NTFS and leaves the operating system and my files (well, whatever is left) and means I can boot into Windows again?
No. Quick means it will remove the file allocation table but not actually remove the data from disk. But this will still show you an empty disk. You need a partiton recovery tool to fix this. And that is not possible with the normal Ubuntu DVD.
I would also suggest to use Windows tools to fix Windows problems. Using Ubuntu for this can have mixed results.
I would also suggest to stop what you are doing and use a tool to restoring your disk. "testdisk" is such a tool but this will only work if you do NOTHING to the disk after you messed it up. Any write to the disk after that is going to kill your data and make it unfixable.
See How to resolve " The harddisk seems too small" with Testdisk deeper search option for a good starting point.