Nothing wrong with asking, but the scope of your question here makes it difficult to answer in sensible timeframe. There's also a lot of valuable content floating around here that already answers different parts of your question, but I'm assuming you've browsed through those, considering that you even started a thread about that.
Something you said in that thread made me cringe a bit, though: "I need to chat less and read more".
As I've been repeatedly told, we all learn in different ways, but IMHO you need to read less and do more. As they say, "the best way to improve at building software is to build software", and that applies to sites too. Build a couple of sites of your own and you'll have a lot better idea about what works for you.. and what doesn't.
Nevertheless, this is an interesting subject, so I'll start by trying to answer your questions briefly based on my typical process:
I don't "create a database and install PW", I've got a script for that. Repetitive tasks are boring and automating them is fun.
I use a previously created site as my starting point. This base site includes common templates, template files organised exactly as I like (something derived from Zend Framework file structure and an implementation of the front controller pattern), various include files (functions.php with common and usually render-related functions etc.) and modules I often end up installing.
I don't know what a "base template code system" is, but if you're talking about template engines (Twig, Smarty etc.) the answer is "never". Those things are are horrible and wrong. If you're referring to something like partials (as in "not full template files but files you'll include within your template files") and helper functions, then yes -- both are useful in their own ways.
The projects we've built before are my "code clip folder".
I could go on and on about this and probably will at some point post something about the directory structure, template logic etc. but don't really have time for that now. If you'd like to know something more specific, please don't hesitate to ask.
You'll definitely get more (and more helpful) answers if you limit the scope of your questions a bit.. though don't be offended if people point you to existing threads either, as that's just the way things work around here. In some ways this forum serves as our collective data bank and the more discussions about same subject are grouped together the easier it is to dig into that subject later