Sometimes it takes a long time. Did they all come from the same litter/cage? If so, they should have it sorted out for the most part. They will have to keep the pecking order so little fights will happen every now and then.
A lot of times one will want to play, clean the other, cuddle, etc. and the other rat will not want it done so they verbally protest. Usually if they are going to hurt each other on purpose it would have happened by now.
I have two almost three-year-old females and they always have little fights. They have never hurt each other, but sometimes they do get loud. Like you said, one will pin the other down, and the other one will just let her know she is not happy. Even though they usually sleep together sometimes they are having a quarrel and they will each sleep some where else. The same with all my other rats. They get angry and pout. So, it is normal.
I have another cage that has my hairless female (Raisin) and my hooded female (Madeline) in it. Madeline still has a baby girl left, Sidney, but she was fine with Raisin coming back home because she was with her before. I have two masked girls I have been trying to integrate in, but Madeline will not have anything to do with it and she gets Raisin on her side. They did fine on play dates, spending hours in the "one home" cage, and they did fine the first day of the move. I thought everything would be fine, so after almost two months of integrating I left them in there over night. When I went to check on them, Morgan (Black masked) had a cut on her back and Mishka (tan masked) had a cut on her lip and belly. I watched them for a bit, and by the poses I knew it was not a dominance thing but a get out and stay out thing. So they did not like living together, but playing together was fine. I will probably never get them all together.
Anyways, good luck with your rats. It should all work out. Just keep an eye on them and make sure the scuffles stay light and do not escalate to something mean. They each have their own personality and their own way of doing things.