You can merge Pencil Notes and PDFs. For example, open a Pencil note or a PDF document then tap the "+" option and "Document Editor". If you tap "+" button then "Import Document" option you will be able to add documents. You can also re-arrange pages using drag&drop gestures.
You can also drag&drop PDF files on the Document Editor view (from the Files app for example) and they will be added to your document.