I quite like How Linux Works by Brian Ward, Its published by No Starch Press
I covers most things in basics, how to comile a kernel, applying pathes, get various networking things sorted like samba shares, network printing. How to sort out cups and various other topics. It doesnt go into too masses of details as each subject can easil have its own book dedicated to that one topic but its a good start for learning the insides.
Also it doesnt give you solutions using a gui, its purly all command line solutions so its not distro specific, it just goes though editing things using nano and things and the various command line tools for setting things up.
In package management it only covers the big two though, RPM and DEB, alhought it does go throuhg compilig software.