You can get Gordian Knot from Doom9.org, it's a free program that walks you through a lot of this. Smartrpper is one included in the package, and one thing it will do is let you pcik size limits for your files... so once it approaches near 4 Gig, it just starts another. Encoding programs like Flask or DVD2AVI have no problems with this.

I guess my point is - NTFS i better than FAT32, and you shold be safe swtiching - but I don't think you HAVE to, not if you're just ripping and encoding movies like I do that is.