Problems between compliant and non-compliant browsers are well-known and well-documented--meaning. What this means is Mozilla follows W3 Standards while Microsoft follows Microsoft standards.
Most of the time, these glitches can be fixed by using external style sheets specific to IE browsers. In other words, you would have a default style sheet, but when IE5, 6, or 7 is encountered, that particular style sheet would be called.
One thing to keep in mind is you only have to change the CSS for the particular element that is not aligned properly. So, the user will always use the default style sheet, but if the user has IE6, for example, maybe the font size for the <h1> tag needs to be smaller--and that change is all you will need to include on the IE6 style sheet.