enclosure filler Qs

As I said, it is a matter of preferance. There is no reason why you need to put it in there, even if the enclosure isn't "perfect". However, in light of the lexan window I suggest you don't use it

Something like this Cascade Audio Deflex pad might be good for an enclosure with a window while gaining some of the benefit of stuffing:

http://www.cascadeaudio.com/prod/deflex.html

I used this in my box because I really didn't want to increase the effective volume but wanted to break up the sub's back wave.  I noticed an increase in sound quality.  They are thin and black, so they wouldn't look bad through a window.