Should I separate my 2 female Russian Hamsters?

I just bought 2 female Russian Hamsters- they were together in the cage at the store and they are gregarious, so I decided to buy them both so they won't be lonely, plus they were the only two in the cage. They were fine, I have had hamsters for 5 years so I know all about them but I am torn about separating them- For the past week, the bigger hammy has been biting the smaller- I mean, like 7 times a day at least, the little one shrieks out in pain- they chirp at eachother, that is not a problem, but now I am really hearing these shrieks!!! Last night, the shrieking was not stopping, and I found the one smaller hammy on her back and the other hammy over her. I know very well that they have a "pecking" order and this is part of their behavior, but I really think she is getting hurt- so last night, when it wouldn't stop, I separated them- they each have their own cage- Should I put them back together? I knoww if they stay apart too long it will be hard to put them back together- what tod