All My Files is literally that: A view of what the system thinks are all your files. That includes all files that OSX shows with YOU as the "owner" of the file. Unfortunately that includes a lot of stuff that I don't need to see, like image files from software I've installed, configuration files for those applications and other "junk" that just clogs up the Finder. I don't find that terribly useful (actually, it's useless) so I recommend you just not use All My Files for anything.
What I think is a better view in Finder is the Home folder. That's the one with your login name and an icon of a little house beside it. Within that folder are the folders YOU should be using, including Documents, where you can put your documents, arranged and located in whatever subfolders you want. You can sort the view in Finder by clicking on the top bar of the columns in any Finder view.
The scroll is what Apple calls "natural." It's a bit controversial, some find it natural (I do) and some don't. The paradigm for it is that if you image the window of, in your case, contacts as a sheet of paper behind that window, and the mouse icon as the end of your finger on a page, then pulling down would take you to the top of the page. It took me about 15 minutes to get the hang of it, but now it does, in fact, seem natural. However, Apple knows not everybody will like it, so in System Preferences, under Mouse, Point and Click, you can de-select natural and go back to the unnatural way things were before Apple changed it.
Just out of curiosity, what were you doing when the keys got hot? Have you installed any "helper" applications on the MBP like MacKeeper, or Clean My Mac? Those kinds of "helpers" actually are mostly useless at best, garbage for all of them and some are actually harmful. OSX has all the maintenance you need, actually. There is one program you'll find recommended here, Onyx but Titanium Software. Search for it and get it from the developer website. Get the proper version for your version of OSX. It's free. You'll need to run it about every 6 months to a year to clean up caches and log files. OSX takes care of the rest.
Oh, and welcome to the forum!
