The Yamaha RX-3060 decodes 11 channels but only has internal power amps for 9.
So you can get 5.2.4 or 7.2.2 out of it as it is. Adding a stereo power amp or using your "proper stereo" to power the fronts gives you the option to go to 7.2.4. Depending on your room size the final .2 or .4 bit may or may not be useful. In a "short" room the .4 speakers may end up too close to be able to discern their individual output. SOme would say that's how it's supposed to work, some would argue that the .4 bit can be overkill. And of course, unless you're using Atmos encoded source discs, it's all a bit moot. Personally, I would go for 7.2.2 rather than 5.2.4, but that's just me.
Atmos speakers work best if they're mounted in or on the ceiling. A .2 setup should have the speakers roughly over but slightly ahead of your main listening position. A .4 setup should see them located in front of and behind your main listening position, at angles between 30 and 45 degrees off horizontal. So if your ceiling is 8 feet high and your ears are 3 feet above the ground when on your couch, the speakers should be between (8-3)=5 and 5/tan(30) = 8-foot 8 inches ahead of and behind your main listening position. Closer than that and the two pairs won't be discernable, further than that and you'll start to notice "holes" in the sound field. My media room is 19 feet long, with the MLP half-way down, and my sepakers are located rounghly 5 feet from the front and back walls, at the quarter-points, so I have roughly a 10-foot gap between them.
Second best seems to be using height speakers mounted where the walls meet the ceiling, angled downwards towards the MLP. I keep on about the Klipsch RP-140SA units - see below - but they're expensive and I'm sure you can figure out what you could do with a set of second hand bookshelf speakers and a tenon saw for much cheaper.
Speakers with drivers in their tops or add-on speakers that bounce sound off the ceiling can be really hit or miss, and a lot depends on your ceiling materials and seating position(s) as anything else, so best avoided.