iBooks is a really nice app for reading books, personally my favorite so kudos to you.
By far the easiest way of transferring eBooks (.ePub file extension) to your iBooks app for iPad or iPhone is via email. You'll need a good ol' fashioned computer for this because Apple doesn't allow you to save files from a download locally to your device (yet).
1. Make sure you have the iBook app installed. If not, you can get it here.
2. Click the link from the download email that we send and hunt down the .ePub file on your computer. Typically this is in the Downloads folder on a Mac and the My Documents folder on Windows.
3. Compose an email to an address account that you have set up on your iPad or iPhone, add the .ePub as an attachment and send away.
4. Open the email you just sent from your iPad or iPhone and hold down on the attached .ePub for a couple of seconds. You'll see a box that pops up where "Open in iBooks" will be an option. Click that and voila! The book is saved on your device and accessible in your iBooks library.