Sometimes you just have to let them duke it out to determine who is boss amongst themselves. As long as they aren't drawing blood on each other they are fine. They are like kids, they will have their disagreements.
Check the other post you made asking the same question. I responded to that one. You may just need more litterboxes. Two cats should have 3 boxes. Always one more then you have cats if there are problems.
If the kitten isn't spayed yet she will become crazy when the hormones and heat cycle kick in and assuming that your older cat is fixed already like she should be, there can be even more problems between the two of them.