It can be overwhelming at first, but once you break it down to the core of what you need, it is not too bad. Here is the basics of what you need.
Line Output Convertor: This is a ~$20 box that takes the signal for the door subwoofer channels native to BOSE and steps it down to RCA signal that an aftermarket subwoofer amplifier can use. This gets installed by an installer usually at the BOSE amp.
Wiring kit: This kit will consist of the following: A main power wire wiuth fusing ran from your battery to the sub amp, a main ground wire that attaches to some location near where you mount the new amplifier, RCAs for taking the signal from the line output convertor and going to the amp, a turn on wire that turns on the new amp, and usually some form of simple speaker wire for hooking your subs to your amp.
This is by far the hardest thing to get right as many opinions of brand and costs change. Some local shops will use a "4 Gauge Power kit" by some crap brand. Don't buy into the cheap, but you also do not need $1000 power wire. Still with major brands. Kicker, Rockford Fosgate, NVX, JL, Metra all make good ones. My rule of thumb wattage wise for most folks is anything under 500 Watts (this is RMS not peak) a good 8AWG kit will do. Anything 500 Watts+ go with a solid 4AWG kit. For reference, AWG is an true measurement of thickness, "Gauge" is technically not accurate sometimes.
Subwoofers: What I normally tell folks is go with the biggest you can afford and deal with. What I mean by that for example is someone driving a Mazda3 with a trunk COULD do 2-12"s in a huge ported box BUT they would use all of their trunk space. Someone in a truck may want HUGE bass but only has room for 1-12". Luckily for CUV/SUV/Hatch owners, you do not have a sealed trunk to overcome. That being said, are you looking for usable hatch space? If so then 2-12"s subs in a huge ported box will take up a lot of space. Output wise all depends on your sub choice.
There are two main difference in the overall output of a sealed versus ported box.
Sealed: Less overall output, punchier bass (good for rock), usually smaller sized boxes
Ported: More overall output, deeper thumping bass (good for rap/electronic), usually larger boxes.
Amplifer: You can play the game of matching amp to subs or the other way around. Keep in mind a good amp is just as important as good subs. You want something that is TRUTHFUL to its power rating. Never focus on Peak/Dynamic, you want RMS ratings. You can do a simple math trick to figure out how much power the amp is theoretically capable of.
If you have "1000Watt Amp" and the amp has a single 30A fuse on it, then 30A is the max that amp can pull before it faults. So given your car being on at 14.4V x 30A = 432 usable Watts. Off brands like Boss, Crunch, will do this. When matching the amp to the sub, look at the sub types and what the amp outputs. For example:
Amp

this means what the amp can output, not what the speakers require.
1000 Watts @ 2-Ohms
500 Watts @ 4-Ohms
So in this case if you picked a 4-Ohm sub that needs 500 watts to work properly your good.
On the other hand if you decided to upgrade and add another same sub later, well now you have 2 4-Ohms subs needed 1000 Watts total (you add them). Luckily when you wire these subs together they come out exactly to that. Planning ahead and save you money later.
Box: Pick a nice sturdy box. Something made out of MDF is normal. Something made of chip board is usually crap. You should not be spending more than about $50 on an OK box.
Here is a setup similar to what I used to suggest to folks.
Amp+Sub :
http://www.sonicelectronix.com/item_117441_JBL-500W-RMS-Dual-12-Subwoofer-Bass-Package.html
Wiring:
http://www.sonicelectronix.com/item_68358_T-Spec-V8-8RAK.html
Line Output Convertor:
http://www.sonicelectronix.com/item_26694_Axxess-AX-ADCT2.html
Box:
http://www.sonicelectronix.com/item_33925_Atrend-12DQV.html
$330 + possible shipping. Not a bad collection
I figure a GOOD installer would charge about ~$175 so around $500 when it is all said and done.
Not to say you cant choose slightly better gear but this gives you a bit of budget room for things like sound deadening or separate sub control ETC. You can also pick a bit better subs and go with something smaller for a more sleek install.