Take a look here. I've posted a few interesting things on the topic of prepositions: http://www.usingenglish.com/forum/te...explained.html
He's in the conference room. - We use "in" for enclosed areas or areas with boundaries. A conference room is an enclosed area.
I like living in this city. - A city has boundaries.
Just leave the reports on my desk. Thank you. - We use "on" for surfaces. A desk is a surface.
There are other ways to use "in" and "on", but these examples, as I believe I recall, represent the "prototypical" uses of "in" and "on", or the primary way in which we use "in" and the primary way in which we use "on".