When you boot from the usb drive, it will ask if you want a clean install or an upgrade.
You want the clean install option.
Then you will have options to erase all partitions on the drive first.
You should do that also since you have nothing you want to keep on the ssd.
When you install windows on the ssd, it is important to leave the HDD disconnected.
You can reattach it later and all your files will be there.
Apps that used the registry(which is now empty) will need to be reinstalled, but data folders are all there.
If you have the HDD connected during the install, windows will place some hidden recovery partitions on it making it all but impossible to remove the hdd later or run without it connected.