I personally try to follow a couple basic rules. .php files should be a single <?php ?> block with nothing outside it, and .phtml files shouldn't use anything but if, foreach, and already defined variables. You'll end up with code that's both cleaner and better structured.
Second, if at all possible avoid Wordpress until you've already got a firm grasp of the language. Wordpress itself has a few decisions that made sense in PHP 4 but are terrible practice now (like using global functions instead of classes) and a few others that, while not technically wrong, were questionable even then (the loop). On top of that, the quality of code in third party themes and plugins varies wildly. If you copy the techniques you see there, you'll learn some awesome tricks, but you'll also learn every bad practice in the book. Until you've got enough experience to recognize the difference, you'll do yourself more harm than good.