Hi Lacy217!
People are talking about two different things here, just so you know.
If you right click on a folder in your Inventory and choose New Clothes > New Jacket from the menu, you'll make a Jacket with a red icon that looks like a jacket. Those use the Upper Body and Lower Body templates. (If you do this, be aware that the upper body has the front on the left and the back on the right, but the lower body has the front on the right and the back on the left. Don't ask me why; it's just the way the Lindens built the UV map, but it's a "gotcha", so be aware of it.

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The disadvantage of these "jackets" is that they cling to the body, since, after all, they are just painted on.
If you want a jacket that bells out, away from the body, then you'd use the Upper Body template and the Skirt Template; but the icon won't show a jacket, and the people wearing it will have to put both pieces on (or wear each one separately.)
If you want the jacket to come just a bit below the top, then I'd recommend the first option.
Using the templates provided by either Chip or myself it's possible (though not easy) to perfectly match the top and bottom of the Jacket. (The one with the red Jacket icon.)
It's simply not possible to perfectly match the top and bottom of the Shirt/Skirt combo, because it "hangs" differently on Male and Female avatars. On the males, it interpenetrates the body at the back, and on the females, there's always a slight gap, all the way around. So, no matter how careful you are, there will be a visible "seam" on some avatars if you have any lines, patterns, or wrinkles that extend over both parts.
On the other hand, it's possible from your question that you were asking about how many layers of clothing an Avatar can have, and if you can arrange them differently.
The answer is that you can have one of each type of clothing. The Undershirt and Underpants are next to the skin. The Socks and Gloves come next, then the Shoes. The Shirt and Pants are in the next layer, and finally the Jacket (which, as stated, uses both Upper and Lower body. The Skirt goes on top of everything else.
So, the Gloves are always over the Undershirt but under the Shirt and Jacket, the Shoes are always over the Underpants and Socks but under the Pants, the Jacket is over everything but the Skirt, and so on.
So, if you want a shirt that's under gloves, you'd actually make an Undershirt with that texture. If you wanted to tuck your pants into your boots, you'd put the texture you want on a pair of Underpants, and so on.
Hope this clear it all up!