I cant really offer alot of advice in terms of how to solve it but I have the same problem.
Please forgive me if I have misread what you have posted but it appears to me that you construct the pages and then see what it looks like?
What I would suggest is to check each browser along the way. Although I personally would focus mainly on IE and Firefox as they ,in my opinion, are the most popular browsers.
Just a little bit of info on Firefox if you didnt know. Firefox adds its own padding which can often lead to mis alignment especially if your using CSS.
There are certain "hacks" which you can implement to take off the padding in IE or add padding in IE etc... Although im not sure where you would find one. Maybe someone else may be able to suggest a website that gives you information on these "hacks"