People have put certain kinds of agriculture into boxes, and so other people think it has to be that way.
Once the plow was invented, larger areas could be grown. It was simplest to make long rows because you can't turn an ox or a horse on a dime.
Some
Permaculture people have been trying for YEARS (well, at least since 1978) to turn it into a religion. It isn't, and never was intended to be, as far as I can tell. It is a GUIDE, not rules engraved in stone.
But, breaking it down to the simplest way, go with ease,
common sense, multifunctionality (if that is a word), and protect resources.
Put the plants that need the most care closest to where you usually are, or where you pass frequently.
Some plants like all the sun they can get, others don't mind some shade in summer. So, if you want to
trellis your cucumbers to keep them growing straight and away from ground bugs and slugs, put it up to get the maximum amount of sun, but the best place
might be the north side of your Zone 1, so it doesn't cast a lot of shade on other plants. Where the trellised cucumbers shade the ground for part of the day is a good place to grow lettuces, so it might not even matter. Just don't put sun/heat lovers in the shade. Hiding your tomatoes from the sun behind a bean trellis will cut down on the amount of tomatoes you get, and they will be slow to ripen.
Improve the soil on a regular basis with organic matter. A soil test from a reliable lab will tell you what nutrients are missing from your soil (no soil is perfect), and go by their recommendations to replace them. Tell them you are growing organically, so they know what kind of specific recommendations to make.
Don't get paralyzed trying to get the design perfect. Perennials and
trees are more difficult to move, so why not wait until next year to decide what the best places for them might be? An asparagus bed would be a pain to move, but rhubarb and blueberry bushes can be moved. Most vegetables are annuals. If you put the cabbages in the 'wrong' place this year, you can plant them in a better place next year. You will be learning all the time. After a few years, a lot of stuff will have become instinctive. A really BAD mistake will teach you a lot, and you aren't likely to do it again!
Pay attention to what is going on in your garden. The best gardeners and permaculturists are good observers. Taking notes is a good thing.
Keep it simple.
Sue