This post will list the various ways to get pdf ebooks (or anything in a pdf) on to your iphone / ipad / ipad mini
there are a few ways to do it:
if its just one or two pdf files then email it to an email address thats configured in your ipads mail account, then just click it and itll open in preview, you can then save to ibooks from there
you can also drag all your pdfs in to itunes on your mac or pc and then go to your the icon for your ipad in the devices menu on the left of itunes, click on it and then go to ebooks.
you can now choose to sync all or select the ones to sync and then hit the sync button
a third option is dropbox :)