Historically I have used a somewhat convoluted method to manage my eBooks. I keep my books in ePub format and load them into my iPhone a few at a time when I tether my iPhone, maintaining the library on my PC. I recently started using a Mac however and of course found that I could not use the iPhone on both computers and thus would have to choose one to sync with and use that computer to load my ePub files. This seems a little counter-intuitive with the whole iCloud push in which I never connect my iPhone to my computer anyway. Time to find a workaround.
The first workaround is to email yourself the ePub file (and I suppose any file that iBooks will read) and then open the attachment using iBooks and it automatically loads the ePub into iBooks. Easy.
Better yet, if you use Dropbox (and I suspect any of the similar services) you can access your ePub files through the service and open them with iBooks, also resulting in the file being automatically loaded into iBook. This method has the advantage or always having access to your entire library so long as you have dropbox and an internet connection. Even Easier.
Note that for this to work your ePub files will have to be DRM-free. I'm sure that you can figure that part out yourself.