How does migration assistant work? I'm considering using Migration Assistant to transfer everything from an old backup of my system to my current system because there are files that went missing when I upgraded my old system to El Capitan.

If I use Migration Assistant to transfer my user accounts, applications, settings, and "other files", will it copy over similar files and make unnecessary duplicates, or will it merge folders to preserve the newest version of a file?

Put another way, say that I have files/folders A, B, and C.
On my old backup, I have A, B, and C.
On my upgraded system, I have A and B, but C was lost in the upgrade process.

If I use Migration Assistant, will it overwrite A and B and add C to my new system from my old system?
Or will Migration Assistant copy over A, B, and C to my new system from my old system, creating two A files, two B files, and one C file, the result of which are unnecessary duplicates?  

Ideally, I'd like to merge folders, so that the newest version of a file is preserved.
Empirically - having done this once &amp; had to pick apart the result - it will make a separate, new account.  

You'll then have to merge across your missing files manually &amp; delete the account when finished.