Firstly I'd suggest having a good read through this car audio site:
www.caraudioaustralia.com/forums (especially in the frequently asked qsts/technical section).
I learned a hellofalot there which led me to changing pretty much my entire audio system since I made some ill-informed decisions initially.
Secondly, I have to put a disclaimer out and say that I don't know the intricacies of a type III but I'm sure there are a few similarities to the beetle. Here is a pic of my kick panels:
They are sealed enclosures (for better midrange response rather than an infinite baffle (like open air unsealed) setup) which have been ported (port diameter and length calculated through a box design software via a fellow on the car audio forum for me) to match the woofer thiele-small specification (all sorts of properties of the woofer which most are over my head - but are used to calculate enclosure design). I painted mine but you could carpet them if you were worried about kicking them, and put grills over speakers to protect them.
Re. tweeter positioning, you want to try and get the pathlengths (distance between your ears and the tweeters) of L and R tweeters as close as possible. So mounting them in the dash causes some problems as the sound from R tweeter will hit your ears before the L tweeter due to smaller pathlength - thus affecting the imaging of the system. By keeping them in the kicks the difference in pathlengths is less and would thus give better imaging. If mounting in kicks, try and keep the axis of the woofer and tweeter the same (which I couldn't do unfortunately) - ie. the angle of the tweeter should be same as the angle of the woofer.
If you go to this link, it details the way I built the kick panels:
http://www.netspot4u.com/~manxclub/gallery/album221?page=1
Re. the sub mounting it under the rear seat is possible - you could make a fibreglass base to maximise box volume and use and mdf top (baffle) to mount the sub. The box volume has a significant effect on sub performance though so trying to optimise the volume for the particular sub is critical if you want the best possible response. There are certain subs which have a small basket depth (ie. don't take up much space) if room is limited - no use if you already have a sub of course.
This is just scratching the surface - could go on and on, but I'm happy to try and answer some of the more basic qsts - but would be worthwhile looking at the car audio forum first.
Cheers
Alan