There in lies the problem most all encounter, even when sellecting the best gear money can buy. Experience and knowledge are where it's at. And good acoustics, setup, tweaking will all be 2/3's of your sound ultimately, regardless.
You likely sit where you have bass challenges, and they correspond with same problems where you sub is, compounding room modes. Also, you likely have phase issues in relation to your speakers from where you sit, and probably volume matching problems...all compounded together.
I'd have to see your setup, and measure.
much more info is needed.
Consulting an acoustical/system setup expert will yield you 200% better results likely. Otherwise, you probably have KAOS with the rest of the speakers in the system, like most.
They all add up, for better or worse...often worse sonically, sadly.
Trial and error is your key if you do it yourself. It might take a lot of time...