I can't speak for the professionals, but I can probably mislead you as well as anyone else.

A lot of what any of us do about layers depends greatly on the weather conditions we typically walk in - there is no one, single, mandatory system for everyone. I walk in the Ohio Valley area, mostly, with some trips to Isle Royale, Shenandoah, and Grayson Highlands/Mt. Rogers thrown in, so what I describe will be what works for me.

The general theory of layering (which assumes cool or cold weather) is a wicking layer, then an insulating layer, then a weather-resistant shell layer. An "unofficial" layer is the warm-weather clothing layer. Some of these things are in your pack, to be put on as needed. (Colin Fletcher's book The Complete Walker has a very thorough description of this.)

There are three things that are permanently in my pack: a spare pair of socks, a rain jacket, and rain pants. The rain gear is waterproof-breathable, which means it doubles as a windbreaker and, on the rare occasions I need them, long pants.

In the summer around here, I wear nylon shorts with a mesh liner (like a swimsuit), with a very thin synthetic (wicking) T-shirt. That eliminates the need to carry spare clothing, including spare underwear, for a weekend. They dry quickly (yep, I've fallen when crossing a creek), and are reasonably cool and comfortable. The synthetic T-shirt elimiantes that "chill" you sometimes get when you're sweaty, stop to rest, and a breeze hits you. I never wear long pants; I find shorts cooler and more comfortable. I've found that a pair of longjohn bottoms under them, or my rainpants over them (or both, when it's cold) are just as functional as long pants.

As we move into fall, I stick a pair of midweight wool longjohns (bottoms and a zip-turtleneck top) in my pack; if it's a little cooler, I'll wear the bottoms under my shorts and/or the turtleneck over the T-shirt. That's my wicking layer. Depending on the forecast, I might also stick a light down-filled jacket in. (That's the insulating layer.) A word about fabrics seems appropriate here. I chose merino wool for no particular reason than I like it better; however, I've used synthetics quite successfully. I have no idea what the difference is between "wool" and "merino wool." I chose the down jacket instead of midweight fleece (say, Polartec 200) or a synthetic-insulation jacket because it's a few ounces lighter, more compressible, and I just like it. Pile, synthetic insulation, and down are equally functional in my neck of the woods. However, if you'll regularly walk where it's wet and rainy, you'll probably want to avoid down since it absorbs moisture more easily (even if it doesn't get wet directly from rain), and loses all its insulating ability when wet.

As it gets really cold, I add a heavier, hooded down sweater (a Polartec 300 layer or heavier insulated jacket would work equally well.) I also toss a pair of light down pants into my pack, completing the insulating layer. Again, fleece or sythetic insulation would work, too. I'm unusual, around here, in carrying the down pants; I rarely if ever hike in them for more than an hour early in the morning - I get too hot. The main reasons I carry them are that they feel good in camp, while I'm cooking and eating, and that they let me get by with a lighter sleeping bag. By wearing the down pants and jacket inside my 30-degree bag, I stay nice and warm in 15 degree weather (inside a tent), and don't have to carry a heavier, 15 or 20 degree bag.

For accessories, I wear a pair of wool liner gloves (inside a pair of fleece-lined mitten shells, if necessary), and a thin, wool wicking stocking cap while hiking. I carry (and wear as necessary) a wool neck gaiter (which I can use as a neck warmer, additional hat layer, or face mask.)If I'm planning to push the limit of my sleeping bag by wearing the down garments in it, I might also toss a pair of down mittens and down booties in my pack.

I'm sure others have different systems, and my system wouldn't be adequate in the mountains in winter (or in northern Michigan or Minnesota, for that matter.) But I rarely hike in conditions where nighttime lows fall below 25 (I stay home if it's colder), and I don't have to deal with 90-degree days with 40-degree nights like you'd have in the desert, either.

So, think first about what kind of conditions you hike in, then put together a system that works for you, using as few pieces as possible. Generally, you'll want to avoid cotton - it actually induces hypothermia when it gets wet - though a lot of people use it in summer around here.

Hope this helps.