There are no down-sides to mixing Atmos speakers with non-Atmos. However, I would take a close look at how well your seating area and ceiling height will fit Dolby's recommendations for Atmos speakers. Read through
this guide. If your seating position vs the speaker placement isn't optimal, don't bother with Atmos. Just get two solid front speakers.
The Klipsch sub is so-so, but you are in an apartment so its not like you can really use a good sub anyway. I would not spend a lot on a subwoofer in your situation. That being said, the aforementioned brands that Pogre suggested are very good.
That Yamaha receiver should be more than adequate to power that system in an apartment.
All the accessories and cables you need should be purchased from
bluejeanscable.com or monoprice.com. Do not buy cables and accessories from stores like BestBuy- the markup is ridiculous, it can cost many times what you need to pay for items, especially if it is from Monster cable, which is no better than generic cable.