you probly need higher pre-out voltage to get a cleaner signal. you'll only usually reach the max voltage using a sine wave @ full volume. when playing music, it will not reach anywhere near rms output.
where the gain knob is set, is totally irrelevant (i.e. a 1/4 way up, or 3/4 way up). it's level matching the output voltage from the hu. hell some ppl will have their gains turned ALL teh way up and still not clip whereas others can go a 1/4 way up and start clipping.
maybe get a better hu, (possibly a new amp) or just build a bigger box.