Yes, I have a basic blank HTML template for each of the standard pages (index, about, contact, blog, 404, single page, etc.) which I use as a starting point. I use snippets (many text editors/IDEs have developers that create snippets with which you can quickly insert basic WP functions and extend them to your own liking). I don't use all the theme files that come as a default with WP.
Next, I create a custom functions.php file where I put all my custom functions in order for them to not get overridden by the next WP upgrade. I use it mainly to disable default functions, add new functions, create custom fields, custom widgets, trim rubbish HTML output from standard functions like wp_pages, wp_nav_menu, categories, and the like.
Good resources are [WPBeginner and [URL="http://perishablepress.com"]PerishablePress](http://wpbeginner.com).
As for books, I recommend Digging into WordPress and How to be a Rockstar WordPress Designer (yes, quite a horrible name, but the book is good).