What is a good starter Ubuntu book?

Well about 99% of all commands are shared between all Distros. This you must have very clear. With this I mean that what you learn in Red Hat, Fedora, Open Suse, Linux Mint, Debian, Gentoo and others, you have a VERY HIGH chance that you can use them in Ubuntu and Vice Versa.

With this said, any place that teaches you some command (Like ls, cat, grep, etc....) will work in any distro.

For common commands I suggest this: http://linux.die.net/

For bash commands I suggest this: http://tldp.org/ and http://www.hypexr.org/

But you also need to know that the stack Network has 2 sites that dedicate themselves to similar questions, https://superuser.com/ and https://unix.stackexchange.com/

For even more in depth to Servers and Security you have https://serverfault.com/ and https://security.stackexchange.com/

Lastly a dedicated Ubuntu Help book would be found here: http://ubuntu-manual.org/downloads and for 10.10 here: https://help.ubuntu.com/10.10/

Regarding files and directories in Ubuntu/Linux, you'll want to read about the Linux Filesystem Hierarchy Standard. As of this post, the current version is 2.3:

• PDF http://www.pathname.com/fhs/pub/fhs-2.3.pdf
• HTML http://www.pathname.com/fhs/pub/fhs-2.3.html

You'll find a listing of directories, required files, purposes of each and various options.

IMO it's a great way to learn the layout of Linux.