In my inexpert opinion.
1) As long as you don't do any thing fancy, mount your disks in the normal way, limit your use to basic file operations, and don't mess with any necessary Windows files on the disk, I doubt there will be any trouble. Every thing I've heard is that the ntfs-3g driver is safe to use.
Of course if there's one thing that's guaranteed in computing, it's that nothing is guaranteed.
2) I don't know if there are any nfts formating programs available in Linux, but I'd do it in Windows anyway. It's probably safer that way. Since it's a patented Microsoft filesystem, they're the only ones who really know everything about it. After it's formatted you can use it safely on Linux, as above.
3) I'm not 100% clear on what you intend here. I wouldn't use an ntfs-formatted partition for my home directory though, since posix file permissions and ownership are rather important things, and you have config files and such in ~/ that may need them. I personally would rely on the KISS principle here and put a small home directory on the main disk to hold your system-important stuff, then mount the two ntfs drives in subdirectories inside it. Or something like that anyway.
Another option might be to create a small ext3 home partition on one of the bigger disks instead for your /home, but then you'd have to have it available every time you log in. I don't know if that's important to you, though it does sound like you intend the two big drives to be removable.
There are also ext2/3 drivers available for Windows, if you want to look at doing it the other way around. I don't know if they support Win7 yet though.