One idea that I've seen posted over and over again in this forum and in the previous ones is that the jaws will always expand with each other as long as you keep them together and in contact (mewing), and as long as you use them often (chewing). This is because the teeth will always try and stay in proper occlusion even as one set of them begins moving. So while you are expanding your upper arch, your bottom arch will begin to move along with those teeth in order to stay locked together with them.

As for why you feel it more in your bottom teeth, that's probably because your upper changes are more along the suture, while your bottom teeth are doing more alveolar or dental changes since there is no suture down there. Over time your lower jaw bone will probably grow to the right size and those teeth will go back into their optimal position (if they aren't there) as long as you keep chewing and mewing. Just a guess though.

Also can you explain more about your expansion routine? How often are you turning the device, which screws are you using, etc.. are you just going by feel?