In the Army, most of our doctrine and other manuals are posted in PDF format. I recently bought a Surface Pro and have been making notes on my publications using Adobe. That said, a few things about the program annoy me, esp having to save the file every time I close the program.

The Army just started to post manuals/doctrine in an Epub format in addition to PDF.

So, I checked out an Epub utilizing Overdrive that I use for library downloads. I can't make highlights or notes using this application.

Before I commit to one format/TTP over the other, what does everyone else use for PDF or EPub documents? I want to be able to continuously use for a few dozen documents even if that means starting over.

I use OneNote frequently but I haven't really tried it with large PDF files. It has a lot of convenient features since it's a Microsoft app. The pen buttons let you erase and bring up the radial menu and you can send things to OneNote from other apps. I think you do need to import or insert the PDF into OneNote.

Drawboard is also a popular app. It costs ~$10. I haven't tried it myself though.

Epub is often easier to read than PDF, but not good for taking notes. You can't do much more than highlight. ReaderPro is a good Epub reader for the Surface.