You might also check out DNNCreative.com and SkinCovered.com for resources.
I'll agree, the book is pretty sparse on usefuul skinning information. They all are. Maybe this will help. Containers are simply visual implementations of the modules you install in a site. They contain the menu for managing the module as well as some kind of separator between modules. Containers are the size of the module, which varies by type of module and what is in it. For a simple HTML/Text module for example, the container will be as wide as the pane and as long as the content requires. Containers don't do positioning, they just "wrap" the module in something pretty.
Panes are how you organize the pages, and yes, they are rectangular. They only are associated with a <TD> tag if you use HTML for the skins and each table cell is a pane. There are many ways to organize the panes, using tables and/or CSS. In general, panes are a way to carve up the page real estate and position modules in those areas. If you need to align modules you may have some playing around to get them lined up as you wish, in all browsers, but it can be done. Not all table cells need to have panes, but wherever you intend to put a module you will need a pane. Skin tags, the third part of the skinning look, don't go in panes normally. So you may have a table with a skin tag [LOGO] in one cell and a pane in the cell right below it, where you will add a Links module from the interface.
It takes some getting used to, and the best way to start is by making small modifications to copies of the default skins until you're used to what's happening. There's no magic, but a good background in HTML layout, especially tables and CSS, will help.
Welcome to the entertainingly frustrating world of skinning DNN! :)
Jeff
Jeff