iBooks is an e-book reader and store that is located uniquely on your iPad, as well as Apple computers and other iOS devices. When you are working with it on your iPad it is a free app available through the App Store, yet the content available through it is a mixture of free and pay items. This is unique since much of the items that you purchase for use on your iPad, such as media from iTunes, is actually stored within a built in mechanism such as the Music system. When figuring out how to store books in the iBooks app you may find that it is actually much more simple than it sounds.
Once you have the iBooks app on your iPad you can hit the Store button in the upper right hand corner of the iBooks library to go ahead and browse the downloadable items. The iBooks store works almost identically to the App Store and the iTunes Store in that it is broken down into different categories, many are featured, some cost money and some are free, and you can browse around. There are unique features such as NY Times, which breaks down their unique bestseller list.
If you find a book you want to download, whether free or for money, you can select it and will be asked to enter in your Apple ID password. When you do the book will appear on your iBooks bookshelf and download, then appearing there for use. When you close out iBooks, the book will remain on this bookshelf for when you re-open it. The question of how to store books in the iBooks app is simply that they stay there once downloaded unless forcefully deleted. The books may be in simply the Books section, or in a collection that you create to organize them on your shelf.
The same principle is true of PDFs. Once you either download them from Safari and open them in iBooks, or put them into your books library in iTunes on your computer before syncing, they will go into your iBooks library and stay there until they are deleted.
What is different about iBooks e-books than simply media on your iPad, or PDFs within iBooks, is that the books are not just stored in your iBooks app, but also in your iBooks account. If you delete your book, or your iPad is cleared out and you have not actually backed it up, then you can download the same book for free since there is a record of having had purchased it. This is going to be similar to App Store and iTunes Store purchasing histories, which allow you to download deleted files that you have already paid for.