How do you directly download ePubs to the ipad ? apologies if this has already been covered but I couldn't find any mention of it.

[circe2]

If the file already is an epub (without compression) you can download it and it will prompt you to choose how to open it (iBooks, etc). Viola! Start reading.

If the file is compressed into a .rar or .zip file as most are, you'll need an archiving program like iUnarchive Lite and possibly a cloud storage program like Dropbox.

When you download the .rar or .zip file, you again will be prompted to choose how to open it. Choose your decompression program and use it. Once you have your epub file, depending on the features of your decompression program, you may be able to choose to open it in your reading program. If not, you should be able to transfer the file to your cloud account and from there access it on your iPad and open with your reading app.

Can you describe your problem in detail? If you want to sync Downloaded Books to iPad in Mac OS X 10.9 Mavericks, you can refer to this guide:http://www.epubor.com/sync-downloaded-books-to-ipad-in-mac-os-x-109-mavericks.html.
If you want to transfer books to iPad, and you can refer to this guide:http://www.epubor.com/how-to-transfer-books-to-ipad.html.

Here's another related thread though for iphone: viewtopic.php?f=1300&t=702879