It depends on which section you are trying to change the margins for. In some sections, changing the margins does nothing. For example, the menu margins don't really work. The taskbar margins and the start menu margins do seem to work.
The content margins effect the location of the text or images that are placed in it. For example, if your icons in the start menu pane are too far to the left, you can adjust the content margins and give it a larger left content margin. Thereby, pushing the icons further away from the border.
The sizing margins adjust the image so that it doesn't stretch or tile wrong. For example if you have a 3 pixel frame on your image, you don't want the frame tiled or stretched. So, you would set a "3" on the sizing margins, which tells Skin Studio
not to stretch or tile that area. You can click the margin setting and then look in the help section to see what type of margin it is(content or sizing). Normally, if it just says "margins", it is a sizing margin. This is because a lot of images don't have content(like arrows).
As far as templates, I don't use them. They are basically someone elses images. But, they are okay to use. But, your skin will not be very original if you use them. Mostly, they are very simple. In my opinion, it is therefore better to develop your own drawing skills before you start making themes.
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