Software to draw on documents?

Preview has some annotation options but in 10.10 it gained a drawing option. https://support.apple.com/kb/PH20218?locale=en_US

You have to check what Preview does in 10.8, but it should do text at least. I doubt that there is an app that annotates everything, but all will work with PDF so if you convert everything to PDF you should be fine. So you just need an app to annotate. Skim (http://skim-app.sourceforge.net) is a favourite for many and you should be fine with it unless you update to the newest OSX. Otherwise something like this: https://itunes.apple.com/us/app/pdf-reader-your-file-viewer/id615956269?mt=12 could work.

For Pen support you need a drawing tablet of some kind (like the Wacom line, most will pretend to be a mouse) and a graphics program (like the open source GIMP), or failing that you need an actual tablet (like an iPad) and you can use your finger or a $5 capacitive pen.

 

Skitch?

Bluebeam Revu?

 

Lots of tools to do this, but I would look at Microsoft OneNote which tends to best match the paradigm you are looking for where it allows you to insert documents and then mark them up but not modify the actual document (this is for better and for worse as you will soon find out). The latest versions of Office all have drawing tools built in but AFAIK this is native to the document and I don't think you can hide the annotations.

This is a LOT more natural on an iPad - especially the Pro models with the Pencil, but people have been doing this for years with cheap capacitive styli and there are a ton of great tools for this on iOS.

 

OneNote is free for Mac. It's in the app store.

I wouldn't turn your nose up because it's Microsoft. It's the best note-taking tool available right now, and happens to be cross-platform and updated very aggressively.

 

You made sense before. I use Acrobat and Bluebeam Revu to do what you're describing.

 

I don't know what website you are talking about? I would just download OneNote and give it a try as it's one of the closer tools to accomplishing what you want. As I mentioned, this is even better on an iPad - either in OneNote or in the many other tools available for iOS.