After installing the “Dropbox sub-folders” add-on, you will have an extra option in the Dropbox configuration section of the UpdraftPlus settings page, as shown at the bottom of this screenshot. Simply enter in the name of the sub-folder which you would like to use:
If you do not see the “Store at:” setting, then you’ve not yet installed the add-on… check out the installation instructions again!
(Note: the apps/UpdraftPlus/ part of the Dropbox path is enforced by Dropbox. Dropbox requires that each application only be able to store data in its own folder. So, your sub-folders will be sub-folders of that path; e.g. apps/UpdraftPlus/MySite1, apps/UpdraftPlus/MySecondSite, etc.).