I'm very new to the Nistune software and slowly finding my way around it. So be gentile with me

I have searched the forum and gone through the Nistune manual and cant really find what Im looking for.
I've tuned up my S14 (SR20DET) with the knock sensor off, next I copied the primary fuel and ignition maps into the knock maps so they are the same and did another pull on the dyno and the power comes down quite a bit.
Why would this happen if the maps are the same? Is there another compensation table somewhere that's knock controlled?
If I start making a map for knock I would think it will only get worse when it flicks to the knock map?
Can I ''dull'' the knock sensor down a bit in the software so it doesn't pick up every little tick of knock?
Any help or tips would be greatly appreciated!