Also, a good amp can do great things at highlighting limitations of your guitar. What kind of guitar do you have? No matter how much you play with your tone controls, a guitar that is suited to the kind of tone you are looking for is the most necessary element in finding the right tone for you. If your guitar simply doesn't have good bass response, your eq settings won't be able to fully boost the bass without making your sound muddy and dull, which could be why it seems like your amp isn't dealing with the bass very well.