It took me a while to figure it out but it's easier than you think.
Once your notes have been uploaded into Evernote from Penultimate, move your notes to a specific notebook on Evernote and the move will be reflected in Penultimate automatically. This is extra simple and can be done on another device like a Mac or PC. Fortunately, after almost one year of messing around with that app, penultimate is back and is once more my favourite app (I keep all my notes in there, it has replaced my old Moleskine)