Technically, unless you're refering to IE4 and IE5.5, there's only 1 IE browser; IE. Every other browser is just a shell.
As far as the issues, tons with IE, but if you keep your HTML simple, things can be over come by using "IE Specific" CSS.
You've seem to be getting frustrated over a very well known problem: IE Box Model. Here's a nice explination as to the IE Box model and what's wrong with it:
It's been a known problem for a good 5+ years, ever since "CSS" itself came onto the picture as mainstream.
Best way to fix it is to create an IE specific CSS file and use:
<!--[if lte IE 6]>
<link relation="stylesheet" type="text/css" href="blah" />
This will also set up your site to be compatable with IE7, too (note: lte means; less than or equal to).