You can do the usb transfer if your iPhone/iPad are jailbroken. But non-amazon ebooks can't be synched with Amazon.
See this link:
https://www.mobileread.com/forums/showthread.php?t=57286
Now I use iFunbox instead of iPhoneBrowser because with iFunbox you can search for application folder with keyword. For example, I search for "Kindle", and I can find the ebooks folder easily instead of having to wade through all the installed apps folder.