Not Sure About it. I know that Mandrake is very similar to Red Hat. But I don't which version correspont to which version.
I know that is better to leave linux to format the partition, But to make sure that is not going to happend again, you could made the partitions with Partition Magic, then when you are installing linux, the only thing that you have to do, is mount the partition and format them again, you dont have to create them. So maybe that will help you to keep the Windows partitions in Windows and the Linux partitions in Linux.
Well, IF you could restore the MBR for W2K, that will be a miracle, because I dont know how to restore it, I have screw up W2k 2 times, before find out where to install lilo. I'm not sure where was suppose to be installed I always forgot where I install it.
I guest that it was in the root partition. Try to made it in this way, so maybe linux will not get both partitions in one.