Does Setup Assistant delete files on the new mac?

I just got a new Macbook Pro, and I'm trying to decide how to transfer all of my files from my old computer to my new one. The problem is that I'm a little paranoid about losing any files on the new computer. I once accidentally wiped my entire system on the old one after an incorrect restore and lost several important folders required for certain applications because they weren't included on the OS reinstallation CD. I don't want that to happen again. I've been reading about Migration Assistant and Setup Assistant, and it seems like they do pretty much the same thing, but I want to make sure that any files currently on the new Mac aren't deleted if I use Setup Assistant to transfer my old files.
Any advice for this particularly paranoid Mac user would be greatly appreciated. Thanks!

Paranoia is understandable; however, misplaced. Just follow the steps in Pondini's Setup New Mac guide.

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