quick advice to 'get you by';
turn bass boost off on the amp.
set the gain between half and 3/4 gain
fire the sub rearward.
adjust the radio's bass or sub control down until the music sounds decent. {if that's all the way down, it'll be ok}
adjust the mid & treble (or just treble) up to your taste. [not all the way up]{if it's almost all the way up, it'll be ok}
you can also fade forward some to hopefully make it sound even better.
lastly, adjust the bass control back up as needed while listening to music.
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aftermarket speakers will most likely make it sound better just by installing them without changing anything else. you could adjust it all afterward to make it sound even better.
6x9s get loud.. but I'm not a fan of mids/highs behind me. and if you simply remove the 6x9s and get it to the point where the 6x9 holes are open to the trunk.. your bass could sound even better than it does