My BFF says she is an atheist but says she prays just in case. I told her that she is not an atheist then. Why would anyone pray to a God they claim does not exist?
I can't say there's no God(s), but i don't believe in this and would never begin to pray to one (or more). I hope for your friend she's chosen the right God should we be wrong. :-)
Most of the people I know in person are Christians, however I have never offered to pray for anyone, thanked God for anything or said God bless you.... just "I'll keep you in my thoughts, Thank you (in general) and bless you because it's polite.... that said, I'm not Christian or an atheist, or anything really.
This situation is not feasible. One who prays to a higher power or deity is not truly atheist. Perhaps a doubter or agnostic, but an actual atheist would dismiss the existence of deities, hence no purpose to pray to one.