Both are filters that let you attenuate certain frequencies above or below a certain point.
A high pass filter only lets frequencies above a certain point pass - i.e. the Highs Pass through the High Pass.
A low pass filter only allows frequencies below a certain point pass - i.e. the Lows Pass through the Low Pass.
Often as well as being able to turn on the filter, you can chose the frequency at which is starts to take affect and sometimes you can chose how much the filter attenuates the sound.
The frequency - 80hz for instance - is the point at which the filter takes affect.
The level - 12dB for instance - is how much the frequencies are attenuated.
For instance, in your example you want to run a sub, so you could set the Low Pass filter to 80hz and the highest level setting, 12dB for example.
That means that anything above 80hz is attenuated by 12dB per octave. Anything below 80hz is left alone and can carry on as normal. So if a 100hz signal is sent, it will be filtered out by the set amount.
Flip that around and you have a High Pass filter. If you set a high pass filter to 125hz at 12dB, anything below 125hz would be attenuated and anything above it can carry on as normal.
As above... in your situation I would recommend using the low pass filter and, if possible, setting it to around 80hz and see how you get on. If you have the ability to adjust it, then by all means do so. Just don't go much higher than 80hz if you can. Use the filter on the amp to start with and leave the head unit filters off.
