The 80Hz setting for Stereo is for a R and L Line Level IN connection. You need only use the single LFE IN on the subwoofer connected to one of the Subwoofer pre outs on the receiver and Bypass should be used as
@isolar8001 mentioned.
The LPF of LFE Output setting in the receiver should be set to 120Hz. Speakers set to Small will default to an 80Hz Crossover but that may not be the optimal setting for each speaker.
Onkyo receivers have presets for Klipsch speakers. If you input your Klipsch Center Channel Speaker and Klipsch Subwoofer models into the Onkyo’s Speaker Combo settings, you will notice it lock them both to 120Hz.
Adjusting the Bass level will have an effect on all channels and the amount of Bass actually sent to the subwoofer from each channel will be determined by their Crossover setting.
Even when the Crossover and Bass level are adjusted to one’s liking, Bass output may still seem low when listening to some music. The Subwoofer level can be bumped up in the QUICK MENU and will return to its former setting when the receiver is put into Standby.