No way to do it the way you are describing, using iBooks. Only iBooks Store content can be set to automatically download on other devices.
You could place your PDF files in DropBox. Several of the better PDF apps will access DropBox directly, making all your files available (as long as you have internet access. You just need to remember to download the ones you want first if your going to be off line.
GoodReader and PDF Expert are my choices. You get a lot more than just a reader.
The DropBox app itself will keep a local copy of any file you mark as a favorite.