Okay. If you have a custom HU, there should be 'pre-outs' or pre-amplified outputs, in the back, with RCA connections. run them to the back of the car, along with a permanent live (wired into the battery through a *rated fuse) and a switch live (best to slave off of the switch live behind the radio) If not, what I did temporarily was slave off the rear speakers. But, you will still need to run a perma-live and switch live to the back. you also need to find a good ground somewhere in the boot, otherwise the electricity has nowhere to go :s
To build a subwoofer enclosure, you need to know the volume of the expansion chamber the subwoofer needs. All subwoofers require different volumes, but you should be able to find them online. then calculate the size box you want to fit best in the boot, and build it. Then find somewhere to safely attach the amplifier and wire it all up. It's easy when you see it all laid out in front of you...