Since QOwnNotes version 1.2.8 note folders are now fully configurable with their paths on your ownCloud server in the settings. This makes this article outdated.
You can create and set an other notes folder with Set notes folder. There again you can store as many notes as you like.
You can later jump back to your old notes folder with Recent notes folders.
If you right click on a note in the note list you can move or copy notes to other folders.
I, for example, created an Archive folder in my notes default notes folder.
You can use the versioning and trash functionality of ownCloud in QOwnNotes for all folders if they all are beneath you ownCloud sync folder.
On a side note, neither the ownCloud Notes web-app nor the CloudNote iOS app are capable of using more than the root /Notes folder. That also the reason why this feature isn't placed more prominently.
Although you can now jump to all visited note folders with a select box above the notes list, this select box is turned off by default and can be turned on in the general settings.