Always wire them back to one location, That means you will be able to connect any room to any other room using two structured cable runs, there are many more thing that can run over CAT cables than just ethernet. I use an CAT 5 KVM, and a USB over cat 5 adapter. Of course I am buying a 3 story house so I might break that rule however if I do I expect I will regret it, there is no good place on the first floor to route all the cables so its ground or top.
You can get single gang sockets that take 3 modules and vertical modules that take 4.
Some links to other wiring threads CAT wiring and this one and this one and this one!
More about hiding cables, here. and here.
The tools you might need is here.