All you need is
1. iBooks installed on iPad
2. iTunes installed on your computer (PC or Mac)
3. This guide to do the transfer
There's nothing complicated in transferring PDF or ebook files to iPad. I don't understand what all the fuss is about.
A lot of apps allow to sync with the associate web app or cloud services like dropbox. Personally I use my business app Beesy and its web platform Beesy.me to upload the pdf on my desktop computeur and display or download it from my iPad app. Since most of the pdf I use are for work, I usually display and edit them within my business app.
Look for app that allow this kind of feature