ePubs and iPads
This sounds fairly inane, but I just figured out how to add ePubs on my iPad. Actually, a friend told me because it wasn't obvious.
You can add ePubs to your library through iTunes. On your iPad, open the iBooks app, and you will see your ePubs there.
Look for your "Book" tab, and drop the epubs in your library as you would drop your mp3 files. Also, iTunes won't accept ".lit" files.
As for PDF files, My friend told me that PDF's work in iTunes, but I tried, and it didn't work. I like to user the GoodReader app. GoodReader won't accept ePubs files. You can make multiple bookmarks. While you can't take notes on digital post-it notes or highlight (like the iBook, see fig.1), you can organize your content into folders (e.g. readForWork, entertainment, tech, see fig.2). There are several controls at the toolbar (fig.3), including "crop," manage bookmarks (you can create multiple bookmarks and name them too, fig.4), search, etc.
How to transfer PDF files to GoodReader
Sometimes you might want to read a report, but not carry your laptop with you. If your report isn't a pdf, just click on "Print." Below is a btn labeled "Save as PDF," which will prompt you to name your pdf and save it to your computer locally. Then open the GoodReader app, and click on the wireless icon (#1 in fig.5), which will prompt a screen giving you an IP-address (#2 in fig.5). Now on your laptop, click command+K simultaneously, and enter the IP-address from your app to the from box labeled "Server Address" and click "Connect." You will see your iPad as a drive. Just transfer your files to your iPad, and Voila.