In general, you shouldn't have to quit SD in the middle. But if you do, Smart Update won't re-copy the stuff that's already copied -- thus, it'll resume.
I don't have much information about what's going on here, but what I'd suggest is running it again.
When it feels like it's stuck, please run:
Code:
sudo lsof | grep SDCopy
in Terminal (copy/paste, then press return if necessary and enter your password, followed by return -- your password won't echo).
The last line or two will show you the file currently being copied. It might give a hint about what's going on...