I had the same problem. I solved it the long hard way.
I purchased the Wrox Book, Beginning CSS Cascading Style Sheets for Web Design, by Richard York and spent 2 months reading and doing examples, from cover to cover.
Now, I have the same problems with layout on master or aspx pages, but can manipulate placement easily by creating controls with no css applied. Later, when I have everything
on a page that I want (controls) I use css style position relative or absolute as needed to place things exactly. Its a long slow process and there oughta be a better way. But until I hear of one, this is what I do.