Hi Cameron,
Welcome.
By all means use your tone controls when necessary. The tweaky British edict (that's where it began, with some of the eccentric British reviewers and magazines) that touching tone controls is forbidden is utter nonsense. Even worse was the trend of manufacturing some "high-end" preamps and amplifiers without any tone controls at all.
Given the wide variation in recording practices as well as the natural decline in lower-bass response of many smaller speakers, tone controls can sometimes be quite useful.
Most smaller bookshelf speakers have bass response that begins to taper off (roll off) beginning at 50 or 60 Hz. The bottom string on an electric bass is at 40 Hz so many bookshelf models are rapidly losing output at 40 Hz. A modest tweek (or an immodest boost!) of the bass control can restore significant output in that region, lending plenty of nice bass and kick drum stuff to playback. Be careful of adding more than 3 dB or 5 dB of bass boost AND turning up the volume--you may overdrive the woofer of a compact speaker.
If you hear nasty "snaps" or grotty distortion, turn down the bass control and/or the volume. But lots of well-designed speakers with good power handling like Axiom's M22s, M3s and M2 bookshelf models can accept 3 dB or more of bass boost with ease at moderately loud levels.
Well-designed tone controls do not introduce distortion of any audible proportions. The best alternative is to have tone controls that can be switched out if audiophiles want to route the signal "direct" to the amp.
I have lots of CDs with anemic or poorly recorded deep bass that can sometimes be given some help with a tweak of the bass control. Likewise, a 2 or 3 dB reduction of treble will sometimes make sibilant CDs quite listenable. If the high-frequency response of your speakers is dull or muted, a treble boost will occasionally make things much more detailed.
Regards,
