iAnnotate is a great app to read and mark up PDFs. One of the best ways to use this app more efficiently is to adjust the settings to your way of working.
The settings can be accessed from a couple of different ways. First, from within the app by tapping the gear icon or tap the Settings icon from your home page. Then, scroll down to the iAnnotate icon and tap it. You will see several different settings specific for that app.
These settings control various ways the app behaves when you use it.
For example, if you have an Apple Pencil, you can have the app automatically recognize when you are using the Pencil to mark up the PDF.
Tap on Annotation and you will see several items to turn on or off. Slide the Apple Pencil Always Inks to on and when you use your Apple Pencil, it will automatically mark up your PDF.
There are other settings that you can use to make for a better experience. You can read the developers article on this here.
In short, no matter which app you may be using, try adjusting some of the settings to increase your productivity.
iPad Notebook 