In addition to what Rawb said, proper set up also asks what you want out of your system. Do you want overexaggerated, piss the people off next to you and down the street bass or do you want it to be authentic and seamless or close to it? There's a guy on YouTube, Steve Meade, who makes the tool Rawb is talking about. This allows you to set the gain on your amp precisely where it should be by detecting when the amp begins to clip and setting it just below that. This is important because despite what the max RMS rated input is of your drivers, people usually kill speakers by underpowering/clipping them than by feeding more power, clean power that is. This happens because an amp merely tries to do what is commanded of it, but if the demands exceed what the amplifier is capable of doing cleanly, the sine wave passing through the voice coil becomes a square wave, approaching straight DC current or something like that. When this happens, the speaker's cone is held at either the top or bottom of it's xmax (speaker cone travel distance) and that builds heat quickly. This then ends up deforming the voicecoil on the former or both the voicecoil and the voice coil former together which then ends up hanging up and sticking on the pole piece. Ever see a woofer that's stuck in place? Yep, that's it.
Anyway, once you figure out what you want out of your system you can begin dialing things in like how Rawb said. In a car, I go for bass that's got just a bit more kick in the 45-120hz region than what is true to the recording. If starting from scratch and assuming we're just running the speaks off the head unit's amplifier, I listen to the full range speakers running full range signal, make sure all equalizer settings or any tone controls are set to flat or bypassed. Probably a good point to tell you that its best and easier on your system to SUBTRACT frequencies, not to boost them. Even just to do a +2dB attenuation on say 60hz will tax your amplifier quite a bit as opposed to subtracting 2dB from all frequency points above it. If the amplifier doesn't "see" the signal, it doesn't have to push it, so what you subtract gives you a little more headroom and the boost where you want it. However, if all you've got is "Bass, Midrange and Treble" settings this won't work, need a parametric EQ.. Anyway, back to gain settings.. Most car stuff isn't equipped with things which tell you when the signal is starting to clip so I just go by ear, carefully. As you approach and get into the clipping region, the sound will become sandy and crackly on the bottom end. Note the volume level on the head unit at this point and quickly turn it back down. Also note if this volume level just before where the sound starts to distort is acceptable. If it's not loud enough, you either have to contemplate getting a four channel amp and possibly different speakers or to see if using that highpass filter will net satisfactory results, if your head unit even has those features. In your case, I think you're running the amps inside the head unit for the factory speakers. I also assume you're running this gear:
TNP212D2KIT MTX Car Subwoofer Enclosure Amp Wiring Pckg | MTX Audio - Serious About Sound®
Looking at the woofer's specs, they're spec'd to run up to 150hz. So depending on how steep you can set your high pass filter (-6 or -12db) I'd be tempted to... Oh.. I just looked up your head unit. First, be sure the output you've hooked your subwoofer's amp to is set to it's subwoofer setting and then set the highpass to 120hz, as it doesn't say how steep the highpass attenuates frequencies above it's setting so 160 would be a bit high for what you've got going on. This will take a lot of load of the tiny amps in your headunit and allow them to play maybe a bit louder but most importantly, cleaner and without as much risk of blowing up. From here, turn the amp on for the subwoofer with the gain around 1/4 from the lowest possible setting. Start listening to a track you know which has a lot of bass, preferably the same one you used to figure out where the car's speakers begin to distort. If it's just you, you'll be doing lots of running to the amp and driver's seat to see where things are at. It's only a 250w amp with those subs you've got so I don't know how comfortable I'd be running the gain up higher than 60%, hell, you might not even get that high before it starts to sound funky. Without that tool from SMD it'll be a lot of trial and error. Ideally, you'd probably be better off with a 600w amp for higher SPL's and more headroom as well as better woofer control. Keep in mind that with audio, 100 watts isn't going to produce 10 times the output of 10 watts. Nope, not at all. Law of diminishing returns right there my friend. This is why speaker/system sensitivity is key. All speakers are (should be and should have it listed somewhere in their specs) rated for SPL output in dB using 1 watt at 1 meter. Higher the better, as it takes roughly six times the power to get just an extra 6 to 10dB out of a speaker rated at say 89dB. With 200 watts into that hypothetical system, you might see peaks of 100 to 102dB. With 600 watts? Maybe something around 108-112dB. This actually comes from my own experiments with amplifiers and a set of JBL L150A's. From this I've learned that you can pretty much take whatever the manufacturer's recommended max RMS power is and double it. Those JBL's didn't really come to life until 250 watts were fed into them and now that I'm running 600w into each, it's near concert level loud & pound with hardly any clipping whatsoever.