I had alternating margin issue sorted out for my thesis, and remember it being easy once I figured it out. Can't for the life ofme remember what it was right now though.
My memory is a bit fuzzy about the details, maybe it was about the inner margins of left-hand side and right-hand side changing. Maybe someone else recognises what I mean? :)
Since Latex is very powerful, I'm sure there is a way to code that behaviour in. But I had spent too many hours already on that project and I was happy with the result anyway, so I stopped investigating.
\documentclass[twoside,a4paper,11pt]{article}