dualboot = linux and win2k/other OS installed?
Right. Or any 2 OSs installed.
mkswap, but the easiest way to manage partitions is with parted and qtparted as frontend to parted. You usually can't check or repair mounted partitions, but you can always boot a distro like knoppix or mepis if you can't umount, e.g. if you want to do something with the / partition.
dosfsck, fsck.msdos, or fsck. fsck is for any type of partition (actually any filesystem). AFAIK fdisk is usually just for creating/deleting/... partitions.
I wouldn't say fat support is alpha. ntfs write support with 2.4.* kernels is alpha
You can't change permissions nor ownership of files on fat, because fat filesystem doesn't support them. However, you can set permissions and ownership for all files on fat or on ntfs when you mount that filesystem. For example: to set permissions to r-xr-xr-x use these options or put them in /etc/fstab:
You need x permissions to enter directories, but you don't want to allow really executing binaries on fat if you don't have any linux programs on fat. Note that with umask you tell what permissions files WON'T have - without 222, i.e. without write for everyone. I forgot what's the deal with the leading zero.
For ownership use uid= and gid= , do a "man mount" for details, but IIRC you just use for example: