OK. Be sure you are using the newest version of iTunes on your PC.
Connect the cable between the PC and iPA. iTunes should start up. If not, start it up.
There are some display options for iTunes. The iPad is either in the left sidebar, or on the right side of the top, above the main window. These options are controlled in the iTunes 'View' menu.
Click on the iPA. If you have a WiFi in your home, on the first Summary option menu on the main window, you can select 'Sync this iPad over Wi-Fi.' That might help your connectivity. You set up the Wi-Fi in system preferences so that the iPA can see your Wi-Fi Net.
Find your eBooks folder(s). In iTunes, select 'Add to Library.' (You can either copy media into the actual iTunes Library, or just link to it. I prefer linking, so I don't make duplicates of everything. This is an iTunes Preference.)
Add the eBooks to iTunes.
In iTunes, on the iPA main window, click 'Books.' Your eBooks should be listed in the first section of Books, with Audio-books below. Put a checkmark on the books you want to go to the iPA. Click 'Sync.'
iTunes will back up purchases first. Then sync. You can watch the activity in the player controller at the top. When it is finished. it will just show an icon or some music title. You can check the iPA while it is plugged in, but be sure to click the EJECT symbol near the iPA name before you unplug it.
The eBooks will appear in the iBooks App. In 'Collections,' make categories for the kinds of eBooks you want: Fiction, Non-Fiction, Sci-Fi, Comedy, etc. by clicking the + New Collection at the bottom of 'Collections.'
At the top of 'Collections' tap 'Books.' Tap 'Edit' They are wiggling. Tap all the books of one genre. The MOVE and Delete words will light up when you tap the first one.
Be sure not to hit DELETE!
Tap MOVE and select the genre you prefer.
Repeat for each genre.
In 'Collections' you can tap the genre and see all the books within.
I hope this works for you.
Good luck.