I think the main problem is that the little amp isn't up to the task of putting out such low notes with the same kind of strength or clarity as the middle-range notes. In order to get such low frequencies to be heard well, you need speakers that are more efficient in the lower frequencies, and you need more power.
A compressor could help a little, in that by flattening out the peaks of the low notes, and turning up the gain, the portions of the signal that the amp CAN reproduce will become louder than they were. Less wattage will be wasted trying to move the speakers for the big low peaks, and more gain will make the upper harmonics of each note easier to hear.
But again, that is not really a solution to the problem--it's just a possible temporary assist.