It would help if we could see what you have done, a link to your site would be nice.

As to pixels, percentages, em's etc....
There are no rules about that. A lot of designers prefer to work in pixels because it gives them greater control. So they usually work on centered fixed widths sites.
Others prefer to work with liquid layouts, that adjust according to resolution. The problem with this is that if on a 800px you want a centered column 10%:80%:10% you will get 80px:640px:80px - now try that on a 1024px screen and you get 102.4px:812.2px:102.4px.

You can split atoms but not pixels so you are left with a slightly lopsided 102:812:110 ratio.

Consider also that each different bowser has different sized borders and slidebars - there is no way you get it right all the time with percentages.

In addition you are using Fontpage; that abomination spawned in the dungeons of MS. The code it generates clearly indicates that it is a child of the "Dark Side" - you will need en exorcist not a programmer to set that one right!