Doesn't dotEpub only do one web page at a time still? I use a Firefox extension called "GrabMyBooks" -
http://www.grabmybooks.com/ - but obviously that's only useful if you use Firefox as your browser.
The other method is to use a web mirroring tool to get multiple web pages saved on your hard disk, then convert those on mass to an eBook. I use "wget" to do the mirroring but it's a very user-unfriendly command line tool so I wouldn't really recommend it.
Andrew