This is what it says in the manual about those knobs. Whatever sounds right/good to you is the correct setting.
Also, read TechNote 101 at egnateramps.com. There is some good information about why speakers sound the way they do.
DENSITY: This control varies the amount of deep, low end in the power amp section and affects both channels. Higher settings create a really big, full low end. Use this control sparingly at high volumes. Excessive bass boost at high volumes can cause some speakers to break up (technical term is “fart out”).
PRESENCE: Adjusts the amount of overall “brightness” in the power amp section and affects both channels. Use this knob sparingly also. To much PRESENCE boost, especially at high volumes, can make your amp sound harsh.
NOTE: The PRESENCE and DENSITY controls are boost only type controls. This means that when the knobs are all the way down, they are not adding or subtracting from the sound. As you turn them up, you are only boosting the low and high content. It’s fine to have them off if that works for your tone.