No, you are correct there, the range of each should not alter speakers that are not playing the affected frequencies. But the bass control will affect both the main speaker and the sub whether you have it set to "both" for bass or with it sending the LFE portion to the sub, within the range of frequencies it modifies. So it will depend on the frequencies affected by the control, but I presume it will be higher (30-80Hz range?) so it will slightly affect a speaker even if it is crossed at 100hz, and it will affect all speakers, not just the sub. I am also saying that modern auto-EQs are pretty good and tone controls essentially are a last resort and likely also means there is a deficiency somewhere else in the basics of the system.