I THINK.... again I haven't been in to comics since middle school... but I think you are both right and wrong
they all happen in the same universe...
but for example... one spiderman has mary jane as the wife, another will have her with someone else.. another will have gwen stacy still alive.. another might have her be the wife... another...... etc etc etc
so while spiderman is happening the same time as x-men, which spider is the REAL definitive story??
lets not even begin with the different plots and restarts and how stories couldn't possibly all line up together..
I think they are all pretty much at random.. I doubt you could line up comic books and tell one large story.. they'd have to write them as such
but if someone wanted to know the one spiderman story, which series of spiderman would be known as the real version?
http://en.wikipedia.org/wiki/List_of_Spider-Man_titles