I just installed my new system and im able to here my subwoofer signal coming from my speakers.

then obviously, you need a low-pass filter.

can u provide more info? little confusing.. r u saying that ur interior speakers are trying to produce low frequencies that ur subs should be handling? or there is unwanted feedback/distortion?
Low pass filter would only help if the problem was reversed.. if the sub was running in full range mode(if u could here mids/high frequencies threw subs)

crap...

http://en.wikipedia.org/wiki/Low-pass_filter

i always get them mixed...

from what i'm reading, it sounds like his normal, full-range speakers are trying to play frequencies that are too low...

so, high-pass would be the ticket if that'* the case.

thats ok... what kind of stereo is this? Monsoon, Bose, all after market?

They distort and crackle, It only does it sometimes though. I mean maybe its not my subwoofer signal cause it does it without the subwoofer level up, but it just started doing it when i put this system in it never did it with my last system.

r ur RCA cables hooked up to Sub outs or rear amp outs? r ur rcas run ontop of ur rear speaker wires from the HU to rear of car? u can be getting feedback from wires being to close together

i've had a loose RCA plug on the amp itself cause those kinds of problems...

i was thinkin something like that, plus i have low quality scoshe RCAs from wal mart.

Just make sure that your wires are ran on the opposite side of the car. Your 99 has the battery up front, so run a power wire on one side, then the RCAs and Remote on the other. It helps to reduce that feedback sound. Also, if your amp or cd player has LPF, you can turn that on too.