I suspect that you have already found Jon's thread about installing the original BookDesigner 4 files and then unzipping the update in the same folder. Plus there is another thread about BookCleaner that adds a few features. Also, checkout the Book Designer best practices in the MobileRead Wiki.
The best guide for creating great books with BookDesigner is HarryT's Guide. I'm not sure where it is posted in the forum so I am enclosing a copy with this post.
I generally keep the paragraph setting at 11 pt Dutch with the Title at 12 point Swiss. I use 10 px margins for the left and right. Your mileage may vary.
Good luck and keep us informed as to your progress.