If you want to read your book on your iPad (or iPhone/iPod Touch), you can use the free iBooks app, or my favorite GoodReader for iPhone and GoodReader for iPad, amongst others.

To add your book to iBooks via iTunes

Using iTunes 9.2 or later, add the books to your iTunes library choosing File menu > Add to Library, or drag the ePub or PDF file to the Books section in the sidebar.

If you like viewing in vertical orientation, I’d recommend the PDF format, whereas the ePub format is better suited to horizontal orientation or small iPhone/iPod Touch screens.

To read these books, simply sync them to your device.

To add your book to GoodReader via iTunes

GoodReader allows you to transfer the book in many different ways, including via USB, wirelessly, or via websites such as DropBox.

To transfer using iTunes, attach your device and click on it in the iTunes sidebar.

Select the Apps tab and scroll down to the File Sharing section.

Select the GoodReader app and drop the PDF file onto the GoodReader Documents section.  They will automatically be transferred to your iDevice and you can open them using the GoodReader app.