Sub Box
 

Looked at Zenclosures sub boxes and seen two of them I am interested in, but wonder which on would sound better the box that the subs face up or the one that faces the rear or should I just go with the custom made box that fists in my spare tire enclosure?

The one that faces back, the one facing up is not going to give you the most out of your sub because it is not going to redirect the bass towards you like the rear one will.