I made a few comments at the tikiwiki.org forums, and will add a bit here. For a full-page-width theme, I'd use the *litecss layout method. This will probably be the default in Tiki 3, finally replacing the current old-school table layout. The tiki.tpl files in templates/styles/feb12 or /darkroom or /tikinewt or /thenews use this method, so could be the starting point. Because the columns are kept in place by means of floats and margins, it's important to make sure the dimensions are consistent. I'm writing up a wiki page on that now, and will post it shortly.
For a single side column, you can just turn off the right column on your Look & Feel admin page; no need for anything special in the files.
I'd avoid customizing template files if possible. They are a bit complex until you're familiar with how they work. If CSS is enough to provide the styling, that'd be easiest. If you want to move things around more than CSS can handle, then template modding is needed, but the downside is that theme-specific template files miss out when the default files are updated, unless you're careful to monitor updates and keep yours in synch.