Puffers produce ALOT of waste so it will take some time for things to zero out. Until they do, I would go with frequent water changes and dosing Prime when you need it (emergency spikes).
As you continue to drop the salinity to 1.008-1.009, your PH will become increasingly difficult to maintain. That is when the baking soda will come in handy. Never add it directly to the tank, always premix it into your pwc
to boost the PH, then take a reading to make sure your not going to sky rocket the ph. A ph of 7.8-8.0 is fine during treatment, the key is to keep it steady.