You'd be fine doing atmos with speakers installed on the wall near the ceiling. 5.2.4 is more than adequate for the effect. As long as your bed layer is solid... dialed in, then putting the Top Front and Top back speakers in place should close the deal on Atmos.
Those seem to be the best positions to get the most of 4-Channel Atmos. Just keep the basic placement guidelines Dolby gives, but install good speakers where the wall and ceiling meet.
If you are going to upgrade to a new reciever, I think I would do the Denon 4500 if you can get a good price on it. The 3600 isn't a bad option... but the 4500 is just personal preference. I think at that level last year, it was more akin to the Marantz SR70xx models whereas the Denon 3x00s were more akin to the SR 50xx models. Its only this year that Denon/Marantz (SoundUnited) started to blur that distinction. But from another current thread here, it seems the 4500 is built a little nicer.