You probably can't, until Apple bring out an iCloud Drive app.
The workaround I would use would be to open it in Goodreader, one of the few iCloud enabled apps (as of their update earlier today). From there you can export it to iCloud Drive.
When you click the save arrow in Mail and the selection box comes up asking where to save, can't you select iCloud Drive fem the favorites on the left then pick your folder?