Grease pencil to VSE pipeline

Greetings cgcookie community!

I have one problem. Don't understand the integrating grease pencil animation into VSE pipeline. 

I start using Blender as my main video-editing tool, right now I help my friend to edit his video-tutorials about programming for games on his Youtube-channel. And very often I need to implement some simple 2d animations for highlighting code lines (using arrows, simple geometric shapes and so on) 

Can somebody share some ideas about that specific topic? 

Thanks in advance.