You can import both PDFs and ePubs from the iBooks app on your Mac.
Start by launching the iBooks app, then select the book you wish to import.
Now drag and drop the book on your desktop to have it copied there.
You can now use various different ways to send the book to Flash Reader, by syncing it with iTunes or by using an app like Dropbox or Google Drive to open it with.
PLEASE NOTE: Only DRM-free (no copy protection) books can be imported, as it is illegal for us to remove the protection.