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I'm assuming you're talking about table sizes when you mention pixel and percentage values. If you want something to stay in place regaurdless of screen resolution you need to use pixel values, percentage values will vary depending on screen size, thus moving the content accordingly.
As for your canvas size, it depends on what resolution you are designing for. But remember, you have to take into consideration the web browser elements; scroll bar, window border, etc. So, I usually subtract at least 30 pixels from the resolution I'm designing for.
For example: if you are designing a site to fit on a monitor set at 800x600, your page width probably should not exceed 770 pixels.
Hope this helps.
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