If I upgrade and choose a non-clean installation, will my personal settings and documents remain? Or my third-party programs?
In a perfect world.... sure.
In fact that would be the primary reason for choosing to "upgrade" rather than selecting a custom clean install, but...
As I implied above, intentions and plans do not always survive very long after first contact.
"Everybody’s got a plan until you get punched on the nose”. <Mohammed Ali>
SO
When considering going forward with "a plan" as significant as upgrading the Operating System of your computer, especially one that contains huge amounts of personal / critical data, then you want to have protected that data and by extension yourself against any and all unintended consequences.
Use one of the many available imaging software products out there, both free and commercial to generate a known good full system image to a safe external source.
AND
By "known good" I mean that after the image is created, make sure that you can open / mount the image and browse it and confirm that you can open and view various items that you consider critical, whether it be documents, images or even music and video.
I would probably even supplement that with a simple backup of all those files and folders you consider critical (probably the contents of your Profile folder) again. Most imaging software supports that type of backup (data / files / folders) as well, but even if you have to perform a simple drag and drop, copy and paste process, you can never be too careful, when protecting your data.