Hi Dave.
HTML and CSS are all you need to build a nice website. JS is handy at times, but it's worth learning to do without it at first, so that you realize that you don't need them, and that they are an enhancement only.
In terms of where to start, focus on the need. Forget all those fancy layouts you could have, or how others are doing everything. Take a break, sit still for a moment and reflect on what your site needs to do with your content. That's the first question to answer: what does your site need to say? What message does it need to convey?
Good web design starts a long way away from code, image editors etc. It starts with the message. Note the main points on paper first. Then build on them, until a picture starts to form of the whole. When you know what the site needs to say, start to organize that content into a meaningful order that would be appropriate for the web. Soon you will find that a structure emerges, and you'll know what pages you need on the site and what content they need to display.
Then start to organize that content on the page in a logical way—and hey presto, you have the beginnings of a design/layout—and one that actually serves your content. (Too many people choose some pretty design and then shoehorn their poor content into any nook it will fit, which is crazy.)
You are then in a good position to start to build your HTML layouts and add a bit of CSS to style them up a bit.
At all points, let the content guide the process. That way, you have fewer decisions to agonize over, and you'll end up with a site that actually does what it's supposed to.
Hope that helps.

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