Unless you are planning to add 5 SATA drives it doesn't really matter. Both are in quite hot areas but without testing the SSD's with thermal imaging or the built in sensor in both locations on this board it's hard telling what is best. I don't know if your usecase is even close to making whatever drive you are planning to use thermal throttle. Also depending on your usecase, I guess, based on their locations, that the top m.2 gets a lot of heat from high CPU loads while the buttom one gets quite hot from high GPU loads.
All in all, testing both locations using the built in heat sensor in your m.2 SSD using a benchmark similar to your usecase is the best way to tell.