I wouldn't change a thing with your ponds unless there is a glaring problem. Do you have any of the rock inside either of the ponds? But just for information, take one of your 'stack rocks' (fieldstone) off to the side and drip a few drop of white vinegar over it. If it 'fizzes' then it might consist of some limestone. At least you will know. What to do about it is another thing. Again, I wouldn't change a thing with either of your ponds especially since they are new and undergoing the cycle. The pH spike could be from many other sources one of which is the time of day and the fact that the lower pond contains fish. What I would do:
Completely test and record the water parameters in both ponds. Test for ammonia, nitrite, nitrate and pH. With the weekend on us and nothing else to do (yeah right) do it several times per day if you can. I am a strong believer in doing more than one test. Sort of like taking a blood pressure test. One reading is nice but three over a 24 hour period gives a better 'picture.'