Setup Assistant launches the first time that you start a new Mac or when you have erased a drive and installed a brand new OS with no accounts or other settings. When you migrate from another computer or external drive into that new system, SA effectively clones everything so that the new system looks exactly like the one being imported.
If you have an existing system that already has accounts in it, Migration Assistant (which you can launch manually) imports all the accounts in the old system or external drive, but keeps the original account(s). This leads to having several accounts in the new system, which can cause problems if the original account and a new account have the same name. That's why it's easier to use SA (when possible) than MA.
