heres what i did in my sei and the costs (from what i remember)
JBL gt4-10 sub (£40 ish was a xmas present though)
amp was second hand off a mate who was upgrading (free) you can get them from 60 - 100 quid second hand though for a decent one or for a new one of a bit of lower quality
wiring kit - £20
3 sheets of 12mm MDF - £5 a sheet ish
2 rolls of car carpet - £15 a roll
screws connectors etc. £10
bit of all purpose sealent knocking round to seal the box.
custom made JBL acrylic grille (optional) - £15
basically i wripped out the old carpet, couldnt stand it and put sound proofing in the wheel well. boxed in the left wheel arch then made a false floor which the sub box slots into. then sealed and carpeted everything and bish bash boosh! its as easy as pie!
the sub box is easy to make if youve got a bit of knowledge! i downloaded this
http://www.ajdesigner.com/speaker/index.php
put in all the details of the sub and you can set constraints for the space its got to fit and it will tell you what size to make the box. dont make two of the dimensions the same size though like the height and depth, plays with the air movement aparently!
my amp is screwed to the box around the left wheel arch and ive got a quick connector on the speaker wires to the sub. so i can disconnect the box and lift the floor up and its out just leaving the amp there! when i was towed home few weeks back i got it all out, my towing eye out, and it all bak in and connected in the time it took the RAC man to get a bottle of WD40 out the van!
just measure your boot, look at what you can buy and add about 50/60 quid for materials to build with and sit there and draw some ideas before you start making! if you want any help give me a shout! i aint far away!
pics of mine: