I have used Adobe's annotating process before. It has certainly helped to prevent me from merely skimming an online document, as Konnikova suggests many readers do with digital material. I use Adobe because I find it easy to navigate and it is free!
The two tools the I use in Adobe are the highlighting tool and the comment ("sticky note") tool. They are located at the top of the screen, in the menu bar. Their icons look like this:
To highlight text, you simply need to select the highlighting button, and then drag your cursor over the text you wish to highlight. After you finish highlighting, you can right click on the highlighted text and select "properties". This will bring you to a box that allows you to choose what color you want your text to be highlighted in. I find this particularly useful when I am annotating different ideas, or when I want to distinguish between different quotes (Bonus: it makes your screen look pretty!)
The commenting tool, or as Adobe calls it, the "sticky note" tool, allows you to add comments in the margins of the text. To use, simply click the speech blurb icon, then click where you want your comment to be. When you do so, a dialogue box will pop up that will allow you to type your thoughts. To read previous comments, simply hover over or click on the icon where you have placed it, and it will display what you have written:
That's pretty much the gist of it! I hope that by annotating documents we become better at reading online material more in depth. Because, let's face it--we cannot all escape to a humble abode, in France, with shaky internet connection, as Miss Konnikova did.