Id use 3/4 inch thick mdf for the box. Its best to use screws and glue to fix it together, you should also go round the inside of the box and run some sealant along all the joins to make sure its airtight. Also make sure you fill the box with some wadding (which is basically like pillow stuffing) so that the sound from your subs doesnt reverberate around the box.
If you make yourself a false floor for your boot then you can screw the sub boxes (and your amp) to that which means they wont move around and makes them less easy to nick.
Finally, ask the place your buying the sub from what the best sized box is. Alternatively look on the sub packaging and it should recommend the best dimensions.
The other option is to just buy the box ready made and carpeted for about £30 and save yourself the hassle.
Rick