Ok so as far as the BB in the water is concerned, water really doesn't harbor enough bacteria for it to make a difference on the system as a whole, in my opinion it really doesn't matter how much of the old water you reintroduce into the new tank, you could honestly just use fresh water from the tap and the fish aren't really going to care.
That being said, it is possible that the PH difference between your tank water and tap water is drastically different depending on how long the system has been established, you can test both waters and if the pH is more than a few points difference then it would be important to equlibriate that difference as closely as possibly so that the fish aren't shocked by pH change. You also obviously want to make sure the temp is as even as possible.
You do, however, want to make sure that any water going into the the tank has been dechlorinated so that you don't kill off the BB. All that being said, there are people out there who will disagree and say that you should mix the old water back in with the new water. I don't personally believe that to be true and I know many hobbyists who don't even acclimate fish besides just a rough temperature acclimation. Also realize that some fish are more sensitive to changes than others, but you have generally hardy fish and invertebrates and I don't think you will have any issues doing this, if you are worried, rest assured you can recycle as much of your old water as you see fit.