Which .css file do I use modify the logo.png size and placement?

I believe you must edit this statement in main.css:

@media screen and (min-width: 81em) {
table.headertable td.logo img {
                              vertical-align:middle;
                              max-height:4em;
}

I determined this by using the DOM Inspector from my browser's Developer Tools. Clicking on the logo reveals its HTML source, the CSS rules applied (and their location), its computed size and how that was calculated, and so on. I couldn't see any other relevant CSS statements applied to the logo or its parents, but I might have missed something.

Oh, and the above is from FM12. I guess FM2015 will be similar, but you never know.