I assume that your new build will be a replacement, not an added pc.
That was not entirely clear in your initial post.
1. A clone is a bit for bit copy. The samsung ssd migration app is a windows C drive mover which I think is a better option if available.
You can download the app and instructions here:
Download various software related to your product, including Samsung Magician, designed for use with Samsung's memory products, and find related information.
www.samsung.com
Also, when you install the 980, also install the samsung nvme driver.
Then move/copy to the 980.
2. When you install the 980 in your new build, it will hopefully boot.
The first thing to do is to install the new motherboard drivers which will come on a cd. (I see that msi is including usb drives now; smart)
When you try to activate, windows will detect a different motherboard and ask you for a new activation code. Windows can be activated on only one pc at a time.
In the activation process, you will have the option to say that this copy of windows has been moved.
3. Unless the used capacity of the source is less than the target, a clone is not going to work.
going from 1tb to 250gb would be a problem.
Past that, you will need a clone utility like macrium reflect to clone to a HDD. The samsung app only works with samsung DDS devices.
If you want, just keep the original 1tb 860 aside in case anything goes wrong.
In time, when you need more space, either use it or buy added storage.
4. Just use your HDD for bulk storage of sequential files such as videos.
It might not be big enough to serve as a backup device. But, backups can be compressed so attaching the hdd via a usb adapter may work, giving you external backup.