The issues being faced by you may be due to difference in file format of ebook that is supported on mac and ipad, so you need to have it converted in the appropriate format. Or Instead of moving the files from Mac to iPad, you can have the ebooks downloaded to iPad directly. For this you need to look for sites namely the novel network and you can find many such sources to download. The ebooks so downloaded could also be played on other devices that support reading the electronic books.

ePub should work fine in iBooks. Check the books are showing up on the books tab in iTunes. If they are then ensure they are selected for syncing when your device is connected or all books are selected.