I also agree re: the comments about the speaker. Just a couple points:
I doubt it is fully broken in yet. You might try the old tricks of playing it near loudly covered in blankets, pointing down into a carpeted floor, etc. If it is an Emi design, think high power, high efficiency, etc. They always take some time to break in. Most of those types of guitar speakers are always pretty 'proud' in the upper mids. Having something that is not so upper mid forward, might really make a big difference in your case for what you are trying to achieve (IMO). At the same time, I have found that most amp manufacturers rarely include a really good quality driver in a stock amp (unless you pay premium $ -- and even then, supposedly 'great' speakers don't always stand up to the hype). Sometimes, if you want a really good one, you just have to go buy one.
I see some similarity here with new Joyo AS owners. It seems like, inevitably, the new user sits down and spins all the dials in every which way, and is basically confounded for the first, I dunno, several hours or even days. Eventually, I had to do as jellodog suggests, just spin the dials after careful listening without having any preconception about what I thought the dials should do. A powerful active EQ (or EQ pedal even) is a very powerful beast to tame sometimes.
It's too bad that the Quilter doesn't offer an ext speaker jack. Just being able to try different speakers on the fly would help clear some of the auditory 'fog' in cases like this. I am a big believer in not being anchored to one particular speaker. Having options = good.