wow.
Dude, your equipment list just makes me sad.
Please, don't take this the wrong way, but I want you to be informed as to what you've got there.
A bandpass box is nothing that it should be at all. You simply cannot stuff any sub into a generic bandpass box and expect it to sound good. All you're going to get is a very narrow, very loud range of mid-bass. If you insist on a bandpass box, you need to have one made exactly to the specs of the subwoofer itself. Trust me, please. You're better off returning that box for a simple sealed box, especially in a car like the MS3. It is a hatchback, and as such it will enhance (if not overdo) mid 80hz frequencies on its own. This is known as "cabin gain". For my sub setup, I chose a unique LMT Eclipse sub, and gave it a large sealed space to work with.
You've got a lot of brands I wouldn't recommend to my competitors, let alone install them in my own vehicle. Again, do not take this the wrong way, I'm simply trying to save you the frustration and disappointment down the road.
First, lets go with Dual. I've not had any trouble with their head units, but then again I've not used many either. However Dual doesn't have their own speaker manufacturing facility, so what speakers you are buying from them (sub) simply is made by the lowest bidder and probably doesn't possess the right characteristics to sound great. I will say that the box choice and design probably makes more difference then the sub of choice though. I've put crappy subs in great boxes and had great results, but I've never seen an excellent sub run well in a crappy box.
Next, lets touch on Power Acoustik...Man this brand is all flash, much like Audiobahn and a whole lot like 100's of other no-name brands out there. You seem to have commented them by their "watts" of power, but in reality you'll never get what they're rated for. Well, unless you are talking about the "WLS" ratings (that stands for When Lightning Strikes), because then they could make their rated power for sure. the big deal on amps is people sell "WATTS", but really its not a wattifier, its an amplifier. In the end, if you have them and can't return them, feel free to use them since amps don't have a whole lot of effect on the final sound quality or quantity produced by a system, but just for future reference pick your amp brands more wisely.
Now, to address several issues you'll deal with along the way of your install:
Since you own an MS3 with the Bose system, you're among the lucky ones that will not need a processor like the RF 3sixty.2 (I have one, I know), instead you only need a quality LOC (line out converter) to get what you want. The Bose head unit actually sends out a good enough signal to run without adjustment, whereas the non-Bose unit definitely needs attention. So, consider running just an Audiocontrol LOC or something similar. Try to avoid those cheapie box things that seem to be popular, find something that actually can properly adjust gains and keep the noise floor down. Audiocontrol gets my vote for this job, and I also like the MTX Re-EQ though it isn't the best value compared with AC products in this field and with your needs.
Next, lets talk about something you completely left off your list: Sound deadening! This car needs it, BAD. Every car needs it in some way, but this one can really see a benefit from the job. Currently the best value I've found in sound deadening comes from Raamaudio. They sell raammat and ensolite, as well as the proper spray adhesive for the ensolite. If you want to do the minimum necessary, order a roll of mat and about 4 yards of Ensolite, and this will do the doors inside and out, and the entire trunk area as well as the rear fender spots behind the plastic, and finally the tailgate. This is what I've done, and it works great. If you want to go a bit more hardcore, feel free to order another roll and more ensolite and do the floor, the rear doors, and maybe the roof if you are so inclined. It will all help.
Lastly, I noticed you are focused on the bass first, then the rest later. I am a big proponent of doing it all at the same time, to make sure you've got balance and proper control of all the frequencies within the audio spectrum. If you need guidance on this issue, simply ask and I'll do my best to help.
My signature contains a few links to help you, and I can provide many more if you want. I recommend asking here rather then PM, so others can easily follow the topic if they need to. Sometimes too many PM's result in a lack of information on the board, where it needs to be.
I, along with a lot of the guys here, wrote up a couple of neat threads regarding these issues directly, so search around and you'll find a lot of great info.
. I happen to have on hand a dual 530watt sub amp, a power acoustik 4 channel 1080 watt sub and a power acoustik 620 watt amp. I figured I would swap the 4 channel amp with the one under the drivers seat and remove the bose woofer and amp. then stick the power acoustik sub and amp in the trunk area. any tips or guides to help me through this? I have no idea about the car. I just want some more thump 
