There's an iTunes app called "FileBrowser" (by Stratospherix Ltd) which lets you put files on your iPad by wifi. I've got it on my iPad, connect to my epub library on my hard drive, select the files I want and copy them over to the iPad.
It even asks you what to do in case if find duplicates. That way you save time by not re-copying files you already have.
When inside File Browser, I find the file I want, click on the button to the right of it and the program will ask me what App I want to open the file in. It will list all the Apps I have that will open an Epub file, and some it won't. (For example, it offers to open the file in Pages, which won't recognize Epubs.) So you may have a bit of a trial and error, but then just chose the one you know will open it.
I have all my epub files on my iPad with this program. Love it.
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