Q: Is there a way to tell when my pre MK3 BASSBOSS subwoofer is being pushed too hard or peaking? 

There are multiple, redundant stages of limiting in the processing and the amplifier. The amp won't clip. This means you don't have to worry about keeping an eye on the back of the subwoofer.

There is no clip light because the amp won't clip. It will compress, but there is no light to indicate when the limiter is active. When the volume stops getting louder, then you've reached maximum output.

Follow proper gain-structure procedures and you won't overdrive your subs. If you don't put clipped signal into the subwoofer, the driver will survive. Here are some dos and don'ts that will help your subwoofers have a long and happy life:

Don't use high-pass or low-pass filters on the signal to the subs because the filters are already built-in.
Don't add gain to the point of clipped signals through secondary mixers or processors.
Do use high-pass filters on inputs for vocal microphones.
Don't use turntables unless they are used to control digital files. Turntable technology was developed before high-output, low-frequency subs and they tend to cause feedback and over-excursion because they are never adequately isolated.

The protect light will flash a coded sequence if the amplifier detects a problem. The one you're most likely to see that indicates some kind of limit is the 6-6, which indicates that the amplifier isn't getting enough power to run at maximum capacity. Usually the remedy is to eliminate power strips, light gauge and/or long extension cords or eliminate other power drains from your subwoofers' circuit.

Here are some of the codes, all of which can be found in the owner's manual...
Long flashes followed by short flashes:

1-0  GROUND NOT CONNECTED: Amp still runs. Blinks 10 times on power-up then stops. Check power cord and outlet wiring.
1-1  LINE HOT AND NEUTRAL REVERSED: Amp still runs. Blinks 10 times on power-up then stops. Check power cord and outlet wiring.
1-2  GROUND NOT CONNECTED IN 240V MODE: Amp still runs. Check power cord and outlet wiring.
2-0 GFI TRIP: Amp shuts down. Power cycle to restore.
3-0 OVERHEAT SHUTDOWN: Amp shuts down. Restarts when temperature falls.
3-3 THERMAL LIMITER ACTING: Gain reduced to limit heat buildup. Amp still runs.
4-7  BROWNOUT AT POWER-UP: Amp shuts down. Power Cycle to restore. Check supply Voltage.
4-8  UNABLE TO START AMPLIFIER: Power Cycle to restore. Check or eliminate power conditioner.
5-0 OVER-VOLTAGE: Amp turns off or won’t start. (Seen on 120V versions when connected to 240V outlets.)
6-0 UNDER-VOLTAGE: Amp turns off or won’t start. (Seen when Generators are overdrawn or long extension cords are in use.)
6-6 LINE LIMTER ACTING: Amp still runs. Output reduced to limit current draw.

Ordinarily you should see only a green LED in Normal operation. Your ears should tell you everything else you need to know!