Its not as difficult as it seems
I'm using a) a Macintosh and b) Marvin for this mini tutorial, with a few screenies. It seems that regularly, people have difficulty with the concepts and activity involved in achieving their end: ie; getting a book from a directory on the computer into a application they read with. The principles here apply to all applications which have the capacity to have books or documents added via iTunes... not all do.
The very first thing you need to do is to recognise that inside iTunes there are TWO ways of seeing your applications.
1) Apps: as listed under the general heading "Library" in your sidebar.
2) Apps: as listed in the horizontal menu which becomes visible when you click on the name of your device.
It is this second Apps list screen we will be looking at. If you try to drag and drop to your first apps listing, or to the apps listing in the top half of the apps screen for your devices, *nothing will happen*. It is NOT possible to add anything to apps in those locations. You must scroll down the device's app screen until you see a section titled "File Sharing" and then look for the app you need, in that list. If its not there... talk to the dev about adding support for File Share, or get a different app. Don't blame iTunes, it can only show you what the developer allows.
Here's what my screen looks like, with Marvin selected.
Now, to get a book from my computer, whether its in some stray directory, or inside Calibre which most of us seem to use, you must click on "Add" as shown in the bottom of the screen, or you can choose to drag and drop into that screen... when the app is selected as per the screenie. I choose "Add", its just a habit, not a necessity.
Here's what Finder on my Mac looks like, when I am selecting a book.
And here's the book now, in iTunes. This took about 10 seconds.
Marvin doesnt show the book right away.
You need to click the little refresh arrow bottom right, and then, there it is
This applies to Marvin, specifically, but you can use the same principle for Stanza, ShubookSE, Megareader, Blio, Bluefire, eBookMobi, i2Reader, Tomes, ReadMe and probably dozens of others I know nothing about. Some, like Marvin, will require an additional activity within the application on the device to show the new books (eg, Shubook has a kind of install from itunes process) but they will all work in very much the same way.
Using itunes to get your books over is the easiest thing in the world, and if you can't be bothered with Calibre (lots dont) then its probably the easiest way to go about getting your books into your device. If you already use iTunes for music management, and audiobooks, its also the only thing that makes sense.
Caveat: If you use iBooks, you can drag and drop onto the books section in "library" of iTunes, or you can use calibre to send to device (I used to use the latter).. but... this isnt about Calibre, theres a whole forum devoted to that... its about using iTunes and not getting unnerved by the negativity which seems to surround it.
I would press you to ignore that, try this out, and then form your own opinion. If you can't make this work, then I have missed a vital step in the howto and would like to know what that is... because it does work, and its easy and quick.