Taller plants go to the north in the northern hemisphere, which includes the U.S. That's so they don't shade the other plants. If the squash is zucchini, plant it in a southern corner or at the edge so the big leaves spill over the sides. Otherwise it can take over a large part of the box. If you plant bush beans rather than pole beans, they can go in the middle and the onions on the low end. Depending on the variety, the peppers will be similar in size to the bush beans.

Here is a link that might be useful: My square foor garden

I recommend getting Mel's book - I got a copy of the original edition for a few bucks on Abebooks.com. Like this

He has some basic layouts that I used in planning mine - it's also my first year with the SFG.

For instance - in one 4x4 bed with a vertical trellis - 2 tomato plants, one each in a square, and 4 cucumbers (2 per square) all growing on the trellis in the back row. Then a couple of peppers or an eggplant in the middle and smaller plants like radish, carrot, mesclun greens, marigolds, parsley, etc in the front two rows.

I think if you follow the spacing guides, and put your taller things to the north, you'll be fine. Plant things you want to eat - and think about how much you'll want of each thing. I planted waaaay too much mesclun greens over the winter and suddenly was drowning in salad. But then it all matured at once, and I wished I had planted crops in succession. I think that's called the learning curve? ;)

Good luck!