IME, ours did....after a couple close calls. How long has the larger one been in the tank, has it est. dominance and taken up with the anemone? We basically did the same thing as you, hoping for a pair. The first week was bad, poor little guy was bullied by everyone. Things calmed down and then we introduced a BTA and it started over again after the larger one began hosting, except it was much worse. The small one was on deaths doorstep. I managed to separate them with a plastic screen hoping to at least nurse the little one back to health to trade back in. After about a week or so, the large one managed to find its way past the screen. Luckily, the small one was well on the way to recovery and the larger decided not to finish the job. We removed the screen and, other than chasing and est. dominance, they did fine. The small one basically stayed on one side of the tank and slowly became bolder, venturing farther and farther across the tank. Finally, about a week or 2 ago, the small one was accepted and is now also hosting in the BTAs (the BTA split during all this). I believe they are now a couple, they no longer quarrel and sleep in the same anemone together.
Yours may or may not get along, anything is possible. But, be prepared for the worst. If you have a QT, you may have to use it. If I hadnt been able to separate them, I'm sure the small one would have died. And I think we were lucky that the larger decided to cease aggression. Maybe cause they were in the same tank and were able to work it out thru the screen, I dont know. I'll put it this way, I had no idea a clownfish could be so aggressive and she now runs the tank. Good luck, I hope things will go well for you. Keep us updated. I may have some pics of the separation, etc. if you want to them.