First of all, you would have to create a second set of files to seed from, as you can't run two torrents from the same set of seeding files (or so has been my experience). Then, yes, a new torrent file would have to be created to refer to the second set of seeding files and link to the second tracker.
I do think that this would be unwise to do on one box though, as it'd put quite a load on the hard drive. When I run two seeds at once, I run one from my tower and one from my lappy. I have the bandwidth to make this an OK proposition; but generally my experience is that seeding is faster overall if you do one at a time.