You can use the Apple Pencil in Evernote — sort of. The stylus can be used with the tool’s sketch feature, which turns whatever you write or drawn into an attachment on a note. It’s not the same as hand-writing the note as you’d do in Apple Notes.
For that type of experience, you’d need to download Penultimate, an Evernote-made handwriting application for iPad that syncs with Evernote, so you can use it to access your files on any device — even if you don’t have Penultimate installed on them.
This isn’t the all-in-one solution many of us were hoping for, but it is the closet thing. This way, all of your hand-written notes are stored in one location that can be edited in the future, and can also be accessed through Evernote on another device.
The main benefit of using Penultimate over the sketch feature in Evernote is that you can quickly run back an edit existing files. It also has a larger suite of stylus features, including wrist-detection, to create a natural handwriting and sketching environment.
You don’t need to use Penultimate, though. You can use other another tool like GoodNotes, then insert the file as a PDF in Evernote. Of course, the limitation here is that this is manual and will need to be done each time you update the file.
Penultimate, on the other hand, integrates with Evernote and automatically feeds the latest version of the file you’re creating into your Notebook in real-time.