The question is: how do you get the book of your iPad or out of your iTunes.
In my case I tested a number of ePub files already stored on my computer. Dropping the files to the iTunes library automatically created a "Books" area in iTunes to which the added files were automatically stored. I then set the iPad device "Books" tab option to "Sync Books > Selected Books" and proceeded to sync the test files to the iPad. Later, when I "purchased" the freebies, I noticed that although they displayed on the iPad, the iPad device directory in iTunes, in the "Purchased on iPad" listings, the did not immediately appear in the "Books" library. However, the next day when I again connected the iPad to my computer I happened to notice that the "purchased" volumes now appeared in the "Books" area of the iTunes library following the automatic "backing up" of the iPad which precedes the initialization sync upon connection. This is all I did. Itunes did everything else on its own and if it doesn't work for you, I simply don't know what else to tell you.
As to getting the content "out of itunes," as I indicated above, once the ePub files were listed in the iTunes "Books" library, I found them to be physically stored on my dedicated iTunes 4TB CalDigit hard drive array and readily available for normal use. I am, of course, assuming the you are using the option to physically store media to iTunes and not using the storage by reference option.