Migration / system setup assistant - basics

I'm seriously contemplating a new desktop machine. It's unlikely it will send my mbp laptop into oblivion, but mostly it will. As I understand it it's possible to completely clone the laptop onto a desktop (system setup assistant) - but then there are software licensing issues. Some of the programs on the laptop need to be ported over and not left on the laptop at all (autocad for ex), others I may want to just get a second license (office).

To make it even more interesting, I have a Parallels 10 VM on the laptop. It needs to stay there as there is one program that will stay on the laptop and not be ported over, so I'll need another parallels license (and w10) for the new desktop. There is one program on the VM that needs to move over to the new desktop. Most everything else can stay on the laptop VM.

Do I run setup assistant - or migration assistant or ?

I do have time machine, Carbon Copy Cloner, and winclone backup files on a external usb drive.

One program I have on the VM is an older program on disk that I have all the key numbers for - but the new desktop won't have an optical disk drive. I'm thinking I'd like to start clean on the windows VM.