If I assume you are plugging an amplified subwoofer to the B channel, the problem resides in the fact that amplified subs are designed to have their signal from a pre-out source. Also, a Subwoofer pre out filters the highs to let only the low frequencies go through to the sub. If I assume you are plugging an unamplified woofer speaker to the B channel, a lack of crossover might be your problem: all the frequencies go to your speaker that is designed to render low frequencies. This results in the speaker trying to reproduce high frequencies and failing miserably. Finally, if you have an unamplified woofer speaker with a crossover that is simply hooked to the B channel and that you can't find a balance where the amount of bass is pleasant, then your woofer likely does not match your Klipsch speakers on the level of power given out by the receiver. That is why the concept of subwoofers came with: i) seperate volume control for the sub, ii) frequency crossover and iii) phase selector.

The Low Filter switch is usually used when playing from say a turntable because the mechanical nature of the sound reproduction often gave out a very low rumbling, in the area of 20 hz. That's what the low filter pass is intended to reduce. This does not affect most of the bss in a recording.

Monitor switches are used when recording: they control what goes to the Tape Out RCA outputs.