I will keep harping on this because it matters a lot, if you want to become adept at using PDFs to be more productive that is. The reason you keep writing on paper to make notes is because it's easy and you don't have to think about it. The reason you don't use PDFs is because it's hard. Why is it hard? Because you have to think about how to do it, and right now you don't know how to do it quickly.
To make notes in Acrobat there are only two things you need to learn how to create quickly: bookmarks and sticky notes.
Think of bookmarks as those yellow tab stickies you put on pages that are in stack. You put those tab stickies there to mark where you have something important you want to look at later. In Acrobat you would create a bookmark to do this. In the graphic below you see the bookmarks panel on the left hand side (the area marked #1). Even if you don't have that panel visible you can create a bookmark with the shortcut CONTROL + B (or COMMAND + B on a Mac, which is what I am using to demonstrate this)
So to create a bookmark you just navigate to the page that you want to bookmark and invoke that command. The bookmarks panel will open and you can name the bookmark whatever you want. You can use bookmarks to break up a document into smaller documents, but that's a whole separate topic.
Now, lets talk about sticky notes. Sticky notes are akin to the marginalia you would scribble next to an important passage. In the world of paper you'd also tab those areas so you can find where you made notes. In the world of Acrobat you can open up the panel and see all your comments listed, and then you can click on any one of them to automatically navigate to that page.
Okay, so sticky notes are a lot more powerful in Acrobat than the ones you make on paper. They can also hold a lot more text than you can scrawl in the margin of a piece of paper. One thing you should know
Acrobat puts the sticky notes under the Comment menu (at least in Acrobat 9 and prior). If you click that menu you'll see (as depicted by area #2 in the graphic above) that the first choice is "Add Sticky Notes." And if you look over to the right you'll see that the shortcut for doing this is COMMAND +6 on a Mac (or CONTROL + 6 on a PC).
So let's review "B" is for bookmarks, and "6" (middle of the keyboard row of numbers) is for creating sticky notes. If you're on a Mac put one finger on the key to the left or right of the space bar (that's the COMMAND key) and then pick a 'B' or '6'. If you're on a PC put your finger on the outermost key from the spacebar (that's the CONTROL key) and then pick a 'B' or '6'.
Practice that until it becomes second nature. Then start weaning yourself from using paper notes; they're inefficient, and they're holding you back.

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