Welcome, I too am new to skinning, still working on my first.
a few things can make life a little easier (for me anyway):
if you leave a little transparency room on your canvas you can also move the image on the canvas to help line up properly to. This is also helpful for certain areas too like the start menu. if your top, bottom, left, and more programs images are against the left edge of the canvas the start menu will render on screen all the way to the left edge of the screen. But if you leave 5 or 6 pixels of transparent canvas to the left of the images it will pull the menu out to the right a little bit, and actually looks better IMO because it doesn't look like the menus left edge is being cut off by the screen.
I would suggest that though it seems a headache, you should play with the margins. They really are easy to understand once you start and it won't take long. open other skins in SKS to look at for reference. of the ones I have looked at the majority of images are set to use Stretch Middle Section / Paint with Margins. Personally I find this easier, someone like voidcore could probably use center/true no margins rather easily due to experience, but I have noticed that your images need to be sized and positioned on the canvas precisely for this to work well. The margins make things easy because images do not have to be the precise size to render properly, stretching will do that for us.
how margins work is really simple. Basically they tell SKS what portion of the image to NOT stretch. take my button below. it has some gloss to the top 1/3 of the image. if you stretch that button vertically the gloss will begin to pixelate into lines and look horrible. To solve this you would use your top margin and bring it down on your image until the margin just covers the gloss line. now when the button stretches the gloss will stay crisp and only the middle and bottom of the image will stretch.
and likewise with this image. this is my pressed button. when it is stretched the lighter areas on the the left and right look terrible. they pixelate into steps toward the middle. so I use the left and right margins and bring them into the image to the point where you see the red overlay (not part of the image, added to show the margins) this way the sides don't stretch and turn into steps.
Text margins are simple to, they move the text around within the area. the text margins tell SKS what areas of the image to NOT render text in.
the last thing I have noticed is Patients young grasshopper. If you want your own images from scratch your going to have to learn how to use the margins.
Good Luck and enjoy the process, OH YA, don't forget to make a pot of coffee...or 2 or 5, your gonna need it...lol