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Complete Noob: Audiobox usb with active bass

Hello, ive been playing bass for a little under 2 years, and recently got an presonus audiobox usb as a gift. So, ive been trying to record, but the sound is off, low notes are distorted, and i cant seem to get the tone i want. So, i was reading around and saw something that said that the audiobox shouldn't be used with active pickups? The only electric bass (i have an acoustic as well) that i have is my first bass, a Cort Action DLX that i got for my birthday 2 summers ago.

So, i have a few questions, in what order should things be hooked up? Bass-My BP200 effects pedal-audiobox, or bass-pedal-amp-audiobox, or bass-pedal-audiobox-amp? I really have no clue since its seems that whenever the amp is involved in any way the sound gets messed up.

Secondly, what should i do to be able to record with good tone? is it safe to use the audiobox? any suggestions are welcome and appreciated. Thanks.