firefox is a standards-compliant browser, meaning that anything that's defined by the
world wide web consortium will work in firefox. IE, however, does not follow web standards--microsoft has a bad habit of trying to define the web for themselves.
the differences between the two really depend on the version you're using. the most recent versions (firefox 3 & ie 7) actually don't have too many differences. the biggest ones are probably padding & rounding. IE sometimes rounds pixels, which causes a lot of misalignment, something that doesn't look to be fixed any time soon.
when you say "scripts" are you talking about javascript, or standard CSS? if it's CSS and you're following web standards in your coding, you shouldn't have too many problems when switching between browsers (though IE will always have some kinks). what you can do in some cases is use "hacks." if it's for myspace, you can use conditional IE properties by putting an underscore in front of the property.
for example, if you want the width of something to be 700 pixels in IE, but 800 pixels in all other browsers, you can use
CODE
div { width:800px; _width:700px; }
it's really only a last-measure resort, because in the future if microsoft decides to no longer read CSS hacks, then it won't work anymore.
if it's for a regular website, you can use regular conditional comments:
CODE
<!--[if IE]>
<link rel="stylesheet" media="screen" href="STYLE SHEET URL" />
<![endif]-->