In the third episode you will have a situation where you need to discover which one is real Emily. Simple answer is that real Emily is the one in front of you.
You have to ask Emily/Emma certain questions, but both of them will know the answers. But they have different vulnerabilities and immunities. Ask Emily in front of you about intimacy and then what was the reason for her visit last night. This will reveal that real Emily is in front of you and the one behind you is Emma.