You will need to create your scripts inside PDN as usual with just the ScriptLab plugin. It leverage's pyrochild's ScriptLab plugin to actually apply a consistent set of plugins on each file, so make sure that's installed first.
I'm sure the future version of PDN will include such a batch automation feature, but I couldn't wait. It bothered me that I couldn't automate the AutoLevel Effect on a folder full of pictures, so I spent the weekend and created a solution. Please donate even $5 if this helps you - it took me about 10-14 hours to complete, and saved me 1 hr manually processing my 154 images. MODERATOR'S NOTE: This plugin may not be compatible with Paint.NET 4.0+.