I don't think you really understand what a honey pot is. A honey pot is a machine with fake services on it that tries to attract crackers and (most of the time) logs them so they can be dealt with.
However, I do commend you on wanting to learn how things work. If you want a good understanding of how unix works, I strongly suggest avoiding alot of main stream Linux distributions and opt for something a little more BSDish (OpenBSD, NetBSD, FreeBSD, Slackware Linux, etc). Another good option for learning about how the operating systems work is Gentoo Linux.
If your focus is security, I'd suggest reading some of the stuff on
Packet Storm. However, don't use that information on machine you are not an admin for.
If you focus is how GNU/Linux works,
Linux From Scratch will show you how things are glued together from a million parts.
If you focus is operating system design and you know how to code, I'd suggest one of the BSD's (OpenBSD for security).