!!!!! After using this workflow for 1.5 semesters I realized that paper and pencil notes feel better for retaining information and no longer use this method !!!!!!
Apps to complete coursework with a Wacom Tablet on Windows. This is a sub-list of my complete workflow which can be found here
Handwritten notes and PDF annotation app with pen input, shape drawing, customizable toolbar, image insertion, audio recording, and multi-platform support.
All lecture notes, assignments, and other handwriting or hand-pdf editing can be accomplished with a wacom tablet and this program
PDF-XChange Viewer is an alternative viewer for PDF files that enables you to view and annotate PDF files. You can add text, sticky notes, and other annotations and save them to the file, which will be compatible with the standard 
Adobe Acrobat Reader.
Export notes from Xournal++ to review and add bookmarks
PDFTK Builder is a free graphical interface to for 
PDFtk, making it much easier to use. It is a easy to use tool to collate (merge), split, encrypt, decrypt, stamp and rotate (only 90°, 180° or 270°) pdf documents.
Combine pdfs. Lecture pdfs can be appended into one file for reviewing entire course history.
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