I'm not entirely sure what you mean when you ask for what kind of implications there would be if a website just used HTML, CSS and PHP. that's all you need to make a website in the first place.

I'm of the mentality that your basic website is simply your HTML and CSS. and you only use PHP to produce and display content, so it's almost even irrelevant to this discussion. that's really all there is to it. after doing that, your website could be considered done.

javascript is something that enhances your website. this means that after your website is finished you can use javascript to add perks. whether it be dynamic/fluid functionality in the form of ajax, or whatever else, javascript is just something to use it enhance a website. at least, that's my take on it.

obviously, when you're that comfortable using javascript, the implementation can go hand in hand rather than finishing the static content (the basic website part) and then adding in the perks. until you're comfortable enough building a website with just HTML and CSS (with PHP for content -- irrelevant as mentioned before), I wouldn't really worry too much about using javascript (or even flash, in your case) in it. tackle one thing at a time.

unless you really know what you're doing, or you get a lot of help (since you are going to school), it is incredibly difficult to take on the task of mastering HTML, CSS, Flash, PHP and JavaScript all at once. I can tell that you're struggling to use each of them, so I would consider taking a step back and focusing on something instead.