Well if you have a spare HD you can do this, towers-of-hanoi style.
You don't say what your current 2nd partition is -- I'll chance it and say it's either /home or perhaps /usr. If it's /usr I don't know if you can pull this off, but /home should be doable.
- What you do is, pop in the extra disk (I'm presuming it's bigger than your second partition).
- Log in as root and mount that new disk as /mnt/newdisk.
- Copy everything from /home to /mnt/newdisk. Do <something brilliant> to preserve access rights.
- Unmount both /home and /mnt/newdisk (do this while being logged in as root, of course, so /home is not used.
- Mount your 2nd disk as /home. (Reboot?)
- Blame somebody else than me if this doesn't work -- I'm not an expert (see my status).
But this is what I'd do, in any case.